Multiple sequence alignment - TraesCS6A01G281200

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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 TraesCS6A01G281200 chr6A 100.000 2552 0 0 1 2552 511038639 511036088 0.000000e+00 4713.0
1 TraesCS6A01G281200 chr6A 88.197 1398 137 12 928 2307 498957391 498956004 0.000000e+00 1642.0
2 TraesCS6A01G281200 chr6A 90.412 1043 97 3 842 1881 523069159 523070201 0.000000e+00 1369.0
3 TraesCS6A01G281200 chr6B 89.486 1731 136 14 842 2552 555340142 555338438 0.000000e+00 2146.0
4 TraesCS6A01G281200 chr6B 87.053 1676 149 33 864 2526 680536953 680535333 0.000000e+00 1831.0
5 TraesCS6A01G281200 chr6B 87.316 544 40 11 289 830 555340929 555340413 1.690000e-166 595.0
6 TraesCS6A01G281200 chr6B 96.667 330 11 0 1 330 555341257 555340928 1.330000e-152 549.0
7 TraesCS6A01G281200 chr6B 87.903 124 11 3 672 793 680537349 680537228 2.650000e-30 143.0
8 TraesCS6A01G281200 chr5D 87.042 1721 132 39 842 2551 450785774 450784134 0.000000e+00 1858.0
9 TraesCS6A01G281200 chr5D 86.609 1725 180 29 851 2552 556144947 556143251 0.000000e+00 1858.0
10 TraesCS6A01G281200 chr5D 82.086 1630 227 37 951 2552 383590589 383592181 0.000000e+00 1332.0
11 TraesCS6A01G281200 chr5D 80.995 442 52 16 2107 2546 558505275 558505686 3.170000e-84 322.0
12 TraesCS6A01G281200 chr7B 86.559 1674 152 35 890 2552 497011126 497009515 0.000000e+00 1777.0
13 TraesCS6A01G281200 chr7B 83.786 1141 117 33 1439 2552 478535452 478536551 0.000000e+00 1020.0
14 TraesCS6A01G281200 chr7B 90.066 151 12 2 2404 2551 164582394 164582544 2.590000e-45 193.0
15 TraesCS6A01G281200 chr7B 88.652 141 16 0 666 806 497023436 497023296 3.380000e-39 172.0
16 TraesCS6A01G281200 chr1B 86.258 1681 173 27 865 2530 616620635 616622272 0.000000e+00 1772.0
17 TraesCS6A01G281200 chr1B 89.661 1180 116 3 842 2019 544730857 544732032 0.000000e+00 1498.0
18 TraesCS6A01G281200 chr1B 86.792 159 21 0 672 830 544730422 544730580 7.260000e-41 178.0
19 TraesCS6A01G281200 chr6D 89.849 1389 116 11 927 2296 356289526 356288144 0.000000e+00 1760.0
20 TraesCS6A01G281200 chr6D 97.030 303 7 1 1 301 370041671 370041369 2.270000e-140 508.0
21 TraesCS6A01G281200 chr6D 91.608 143 12 0 2409 2551 356288099 356287957 5.570000e-47 198.0
22 TraesCS6A01G281200 chr3B 87.918 1465 156 12 845 2296 560337254 560335798 0.000000e+00 1705.0
23 TraesCS6A01G281200 chr3B 89.209 936 91 6 1385 2310 96821846 96820911 0.000000e+00 1160.0
24 TraesCS6A01G281200 chr3B 89.820 167 12 4 666 830 651601699 651601536 2.570000e-50 209.0
25 TraesCS6A01G281200 chr3B 79.933 299 31 12 2255 2549 96820907 96820634 2.590000e-45 193.0
26 TraesCS6A01G281200 chr4D 83.524 1396 173 36 1196 2552 478726777 478728154 0.000000e+00 1251.0
27 TraesCS6A01G281200 chr4D 85.018 821 84 19 1741 2552 16748150 16747360 0.000000e+00 798.0
28 TraesCS6A01G281200 chr7D 85.620 1217 92 38 1351 2549 199360843 199359692 0.000000e+00 1201.0
29 TraesCS6A01G281200 chr7D 80.471 425 37 18 2136 2549 551850660 551850271 1.490000e-72 283.0
30 TraesCS6A01G281200 chr4A 86.429 899 92 13 1420 2307 583807060 583807939 0.000000e+00 957.0
31 TraesCS6A01G281200 chr4A 84.333 300 18 14 2255 2552 583807946 583808218 1.510000e-67 267.0
32 TraesCS6A01G281200 chr5B 86.099 892 75 23 1673 2549 65289881 65290738 0.000000e+00 915.0
33 TraesCS6A01G281200 chr5B 87.578 161 19 1 668 828 65280015 65280174 4.340000e-43 185.0
34 TraesCS6A01G281200 chr3A 89.933 149 14 1 2404 2551 21363636 21363488 9.320000e-45 191.0
35 TraesCS6A01G281200 chr3A 80.000 125 14 10 2274 2393 21363744 21363626 5.850000e-12 82.4
36 TraesCS6A01G281200 chr2A 86.486 148 17 3 2404 2549 112733477 112733623 2.630000e-35 159.0
37 TraesCS6A01G281200 chr2D 86.301 146 17 2 2404 2549 112089472 112089614 3.400000e-34 156.0


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 TraesCS6A01G281200 chr6A 511036088 511038639 2551 True 4713.000000 4713 100.000000 1 2552 1 chr6A.!!$R2 2551
1 TraesCS6A01G281200 chr6A 498956004 498957391 1387 True 1642.000000 1642 88.197000 928 2307 1 chr6A.!!$R1 1379
2 TraesCS6A01G281200 chr6A 523069159 523070201 1042 False 1369.000000 1369 90.412000 842 1881 1 chr6A.!!$F1 1039
3 TraesCS6A01G281200 chr6B 555338438 555341257 2819 True 1096.666667 2146 91.156333 1 2552 3 chr6B.!!$R1 2551
4 TraesCS6A01G281200 chr6B 680535333 680537349 2016 True 987.000000 1831 87.478000 672 2526 2 chr6B.!!$R2 1854
5 TraesCS6A01G281200 chr5D 450784134 450785774 1640 True 1858.000000 1858 87.042000 842 2551 1 chr5D.!!$R1 1709
6 TraesCS6A01G281200 chr5D 556143251 556144947 1696 True 1858.000000 1858 86.609000 851 2552 1 chr5D.!!$R2 1701
7 TraesCS6A01G281200 chr5D 383590589 383592181 1592 False 1332.000000 1332 82.086000 951 2552 1 chr5D.!!$F1 1601
8 TraesCS6A01G281200 chr7B 497009515 497011126 1611 True 1777.000000 1777 86.559000 890 2552 1 chr7B.!!$R1 1662
9 TraesCS6A01G281200 chr7B 478535452 478536551 1099 False 1020.000000 1020 83.786000 1439 2552 1 chr7B.!!$F2 1113
10 TraesCS6A01G281200 chr1B 616620635 616622272 1637 False 1772.000000 1772 86.258000 865 2530 1 chr1B.!!$F1 1665
11 TraesCS6A01G281200 chr1B 544730422 544732032 1610 False 838.000000 1498 88.226500 672 2019 2 chr1B.!!$F2 1347
12 TraesCS6A01G281200 chr6D 356287957 356289526 1569 True 979.000000 1760 90.728500 927 2551 2 chr6D.!!$R2 1624
13 TraesCS6A01G281200 chr3B 560335798 560337254 1456 True 1705.000000 1705 87.918000 845 2296 1 chr3B.!!$R1 1451
14 TraesCS6A01G281200 chr3B 96820634 96821846 1212 True 676.500000 1160 84.571000 1385 2549 2 chr3B.!!$R3 1164
15 TraesCS6A01G281200 chr4D 478726777 478728154 1377 False 1251.000000 1251 83.524000 1196 2552 1 chr4D.!!$F1 1356
16 TraesCS6A01G281200 chr4D 16747360 16748150 790 True 798.000000 798 85.018000 1741 2552 1 chr4D.!!$R1 811
17 TraesCS6A01G281200 chr7D 199359692 199360843 1151 True 1201.000000 1201 85.620000 1351 2549 1 chr7D.!!$R1 1198
18 TraesCS6A01G281200 chr4A 583807060 583808218 1158 False 612.000000 957 85.381000 1420 2552 2 chr4A.!!$F1 1132
19 TraesCS6A01G281200 chr5B 65289881 65290738 857 False 915.000000 915 86.099000 1673 2549 1 chr5B.!!$F2 876

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
487 528 0.026415 AGGGATAGAGGGGGAGAGGA 60.026 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 2466 0.518636 CAGGCACCAGTTCGTCAATG 59.481 55.0 0.0 0.0 0.0 2.82 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
75 76 1.457455 GGAGGAGAGCTGGGAGAGG 60.457 68.421 0.00 0.00 0.00 3.69
80 81 2.445654 GAGCTGGGAGAGGAGGGG 60.446 72.222 0.00 0.00 0.00 4.79
129 130 1.762222 CTAGGCGGCGGATTTTGACG 61.762 60.000 9.78 0.00 41.93 4.35
288 289 2.016961 CATCAACGCCCTCGATTGG 58.983 57.895 0.00 0.00 39.41 3.16
311 312 1.016627 TGCCGATTTGCTATCAGTGC 58.983 50.000 0.00 0.00 0.00 4.40
317 318 4.332543 CCGATTTGCTATCAGTGCTACAAA 59.667 41.667 0.00 0.00 0.00 2.83
347 388 2.245714 GCACGTGCAGGCTTAGAAGC 62.246 60.000 34.52 5.66 45.30 3.86
370 411 2.224769 CCCCTGGTTCAAGCTTAGTTGA 60.225 50.000 0.00 0.00 34.56 3.18
372 413 3.888930 CCCTGGTTCAAGCTTAGTTGAAA 59.111 43.478 0.00 0.00 45.65 2.69
373 414 4.340950 CCCTGGTTCAAGCTTAGTTGAAAA 59.659 41.667 0.00 0.00 45.65 2.29
374 415 5.163457 CCCTGGTTCAAGCTTAGTTGAAAAA 60.163 40.000 0.00 0.00 45.65 1.94
430 471 2.631418 ATGACTTAGACACGACACGG 57.369 50.000 0.00 0.00 0.00 4.94
438 479 0.725118 GACACGACACGGACGAGAAG 60.725 60.000 0.00 0.00 34.70 2.85
442 483 1.050767 CGACACGGACGAGAAGAAAC 58.949 55.000 0.00 0.00 0.00 2.78
462 503 4.104383 ACAGAAGGGCAATTGAGAAAGA 57.896 40.909 10.34 0.00 0.00 2.52
484 525 1.790157 GAAGAGGGATAGAGGGGGAGA 59.210 57.143 0.00 0.00 0.00 3.71
487 528 0.026415 AGGGATAGAGGGGGAGAGGA 60.026 60.000 0.00 0.00 0.00 3.71
490 531 2.157926 GGGATAGAGGGGGAGAGGAAAT 60.158 54.545 0.00 0.00 0.00 2.17
495 536 2.849318 AGAGGGGGAGAGGAAATCAAAG 59.151 50.000 0.00 0.00 0.00 2.77
516 557 2.482721 GGATGTGTGTAAGGGTTGAACG 59.517 50.000 0.00 0.00 0.00 3.95
519 560 2.093606 TGTGTGTAAGGGTTGAACGTCA 60.094 45.455 0.00 0.00 0.00 4.35
542 583 1.362355 GACAACCACCGCAAAAGGG 59.638 57.895 0.00 0.00 35.02 3.95
570 611 2.292828 AGGACCTGGAACAACAATGG 57.707 50.000 0.00 0.00 38.70 3.16
593 634 4.410400 GGGTTGAGGCTCCGGTGG 62.410 72.222 12.86 0.00 0.00 4.61
613 654 2.101249 GGAAGAGAGAGGCTGTCATGAG 59.899 54.545 14.66 0.00 0.00 2.90
628 669 6.358974 TGTCATGAGAACAAATGTAGGAGA 57.641 37.500 0.00 0.00 0.00 3.71
644 685 3.858135 AGGAGAAGAAGTTGTGTAGGGA 58.142 45.455 0.00 0.00 0.00 4.20
670 711 8.058847 AGAAACAAATAATCATACCTTAGGGCA 58.941 33.333 2.32 0.00 35.63 5.36
794 835 4.154347 CCCTCAGCCTGGCTCGTC 62.154 72.222 20.49 0.00 36.40 4.20
796 837 2.729479 CCTCAGCCTGGCTCGTCAT 61.729 63.158 20.49 0.00 36.40 3.06
814 855 3.369756 GTCATAAACTGTCGAATCGGCAA 59.630 43.478 12.08 0.00 42.08 4.52
817 858 3.471495 AAACTGTCGAATCGGCAATTC 57.529 42.857 12.08 1.90 42.08 2.17
830 871 1.137086 GGCAATTCCTAGCGAGTCAGA 59.863 52.381 0.00 0.00 0.00 3.27
831 872 2.418746 GGCAATTCCTAGCGAGTCAGAA 60.419 50.000 0.00 0.00 0.00 3.02
832 873 3.262420 GCAATTCCTAGCGAGTCAGAAA 58.738 45.455 0.00 0.00 0.00 2.52
833 874 3.062774 GCAATTCCTAGCGAGTCAGAAAC 59.937 47.826 0.00 0.00 0.00 2.78
834 875 4.499183 CAATTCCTAGCGAGTCAGAAACT 58.501 43.478 0.00 0.00 42.42 2.66
836 877 1.202582 TCCTAGCGAGTCAGAAACTGC 59.797 52.381 0.00 0.00 38.74 4.40
837 878 1.634702 CTAGCGAGTCAGAAACTGCC 58.365 55.000 0.00 0.00 38.74 4.85
838 879 0.109272 TAGCGAGTCAGAAACTGCCG 60.109 55.000 0.00 0.00 38.74 5.69
839 880 1.372997 GCGAGTCAGAAACTGCCGA 60.373 57.895 0.00 0.00 38.74 5.54
858 1174 0.108615 AATCGTCCTTCACTCAGCCG 60.109 55.000 0.00 0.00 0.00 5.52
861 1177 1.666011 GTCCTTCACTCAGCCGTGA 59.334 57.895 0.00 0.00 41.82 4.35
862 1178 0.247736 GTCCTTCACTCAGCCGTGAT 59.752 55.000 2.46 0.00 42.91 3.06
908 1232 2.469516 CCGGTAAGCAACATCGCCC 61.470 63.158 0.00 0.00 0.00 6.13
922 1246 0.397535 TCGCCCGTCCCCTAAGTTAT 60.398 55.000 0.00 0.00 0.00 1.89
1018 1343 0.901827 TATGGACGCACAGATGTGGT 59.098 50.000 14.44 10.24 45.72 4.16
1024 1349 1.003118 ACGCACAGATGTGGTTGGTAT 59.997 47.619 14.44 0.00 45.72 2.73
1029 1354 4.022416 GCACAGATGTGGTTGGTATTTCAA 60.022 41.667 14.44 0.00 45.72 2.69
1123 1448 4.900652 AGAGACCTGTCATCAGATATGCTT 59.099 41.667 0.00 0.00 43.76 3.91
1217 1550 7.176340 GGCTCTATGGATGCTTAGAATGAAAAT 59.824 37.037 10.42 0.00 0.00 1.82
1258 1591 0.487325 TCAGACCTTCAGGACCAGGA 59.513 55.000 3.37 0.00 38.94 3.86
1349 1683 4.514401 CATAACCAGAGGTTCAGGGTTAC 58.486 47.826 4.44 0.00 43.05 2.50
1367 1701 0.253610 ACCCACAACACGTTCAGGAA 59.746 50.000 0.00 0.00 0.00 3.36
1455 1796 2.566833 TGATCAAGTCACCAACTGGG 57.433 50.000 0.00 0.00 38.58 4.45
1557 1908 6.774170 TGCTTGATATGCTTGGATAGTTCAAT 59.226 34.615 0.00 0.00 0.00 2.57
1738 2094 0.830648 GTCCACCTATGTGCTGGCTA 59.169 55.000 0.00 0.00 41.35 3.93
1810 2168 3.134623 TCGTCCTAATGGCATCAACATCT 59.865 43.478 0.00 0.00 0.00 2.90
1881 2239 2.716424 TGTTCTTCCACCCTTCAGGAAT 59.284 45.455 0.00 0.00 42.62 3.01
1913 2271 4.389077 CCATCTGAACGAGTTCTTTGGTAC 59.611 45.833 15.80 0.00 40.14 3.34
2099 2466 1.831286 CTGGATCCTGCAATGGGGC 60.831 63.158 14.23 0.00 0.00 5.80
2212 2589 3.137544 TGGAAGAACAAAAGGCTGGAGTA 59.862 43.478 0.00 0.00 0.00 2.59
2214 2591 4.505039 GGAAGAACAAAAGGCTGGAGTAGA 60.505 45.833 0.00 0.00 0.00 2.59
2240 2617 1.678101 GCAATGTGGGATAACAGAGGC 59.322 52.381 0.00 0.00 32.52 4.70
2312 2852 2.801111 GGAAGACGAAGAGGAACAACAC 59.199 50.000 0.00 0.00 0.00 3.32
2313 2853 2.528041 AGACGAAGAGGAACAACACC 57.472 50.000 0.00 0.00 0.00 4.16
2314 2854 1.760613 AGACGAAGAGGAACAACACCA 59.239 47.619 0.00 0.00 0.00 4.17
2343 2938 7.518188 ACAAAAGAGGTAAGATGAAGAGGAAA 58.482 34.615 0.00 0.00 0.00 3.13
2395 3024 5.186996 CCATTTGGCTCTTAATAATGCGT 57.813 39.130 0.00 0.00 0.00 5.24
2396 3025 6.312399 CCATTTGGCTCTTAATAATGCGTA 57.688 37.500 0.00 0.00 0.00 4.42
2397 3026 6.142817 CCATTTGGCTCTTAATAATGCGTAC 58.857 40.000 0.00 0.00 0.00 3.67
2398 3027 6.017109 CCATTTGGCTCTTAATAATGCGTACT 60.017 38.462 0.00 0.00 0.00 2.73
2399 3028 5.984233 TTGGCTCTTAATAATGCGTACTG 57.016 39.130 0.00 0.00 0.00 2.74
2400 3029 3.807622 TGGCTCTTAATAATGCGTACTGC 59.192 43.478 3.22 3.22 46.70 4.40
2401 3030 3.186613 GGCTCTTAATAATGCGTACTGCC 59.813 47.826 7.13 0.00 45.60 4.85
2402 3031 3.807622 GCTCTTAATAATGCGTACTGCCA 59.192 43.478 7.13 0.00 45.60 4.92
2403 3032 4.452455 GCTCTTAATAATGCGTACTGCCAT 59.548 41.667 7.13 0.00 45.60 4.40
2404 3033 5.389935 GCTCTTAATAATGCGTACTGCCATC 60.390 44.000 7.13 0.00 45.60 3.51
2405 3034 5.853936 TCTTAATAATGCGTACTGCCATCT 58.146 37.500 7.13 0.00 45.60 2.90
2406 3035 6.288294 TCTTAATAATGCGTACTGCCATCTT 58.712 36.000 7.13 1.39 45.60 2.40
2407 3036 7.438564 TCTTAATAATGCGTACTGCCATCTTA 58.561 34.615 7.13 2.29 45.60 2.10
2408 3037 7.929245 TCTTAATAATGCGTACTGCCATCTTAA 59.071 33.333 7.13 6.48 45.60 1.85
2409 3038 8.615878 TTAATAATGCGTACTGCCATCTTAAT 57.384 30.769 7.13 0.00 45.60 1.40
2410 3039 9.713713 TTAATAATGCGTACTGCCATCTTAATA 57.286 29.630 7.13 0.00 45.60 0.98
2411 3040 8.615878 AATAATGCGTACTGCCATCTTAATAA 57.384 30.769 7.13 0.00 45.60 1.40
2412 3041 8.792830 ATAATGCGTACTGCCATCTTAATAAT 57.207 30.769 7.13 0.00 45.60 1.28
2413 3042 5.922739 TGCGTACTGCCATCTTAATAATG 57.077 39.130 7.13 0.00 45.60 1.90
2414 3043 4.213270 TGCGTACTGCCATCTTAATAATGC 59.787 41.667 7.13 0.00 45.60 3.56
2438 3067 6.390721 CGTACTGCCATTTGATAGTAGCTAT 58.609 40.000 0.00 0.00 0.00 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 168 2.111878 GGACCCAGATGGCATCCG 59.888 66.667 23.33 13.79 37.83 4.18
288 289 0.953727 TGATAGCAAATCGGCATGGC 59.046 50.000 9.69 9.69 35.83 4.40
311 312 3.796178 ACGTGCTTTGTTTGCATTTGTAG 59.204 39.130 0.00 0.00 42.69 2.74
317 318 0.179116 TGCACGTGCTTTGTTTGCAT 60.179 45.000 37.59 0.00 42.69 3.96
374 415 5.773239 TCGCGTCGAAGATTTCTATTTTT 57.227 34.783 5.77 0.00 40.67 1.94
375 416 5.518847 TGATCGCGTCGAAGATTTCTATTTT 59.481 36.000 5.77 0.00 39.99 1.82
376 417 5.041287 TGATCGCGTCGAAGATTTCTATTT 58.959 37.500 5.77 0.00 39.99 1.40
377 418 4.607955 TGATCGCGTCGAAGATTTCTATT 58.392 39.130 5.77 0.00 39.99 1.73
378 419 4.224715 TGATCGCGTCGAAGATTTCTAT 57.775 40.909 5.77 0.00 39.99 1.98
379 420 3.685836 TGATCGCGTCGAAGATTTCTA 57.314 42.857 5.77 0.00 39.99 2.10
380 421 2.561733 TGATCGCGTCGAAGATTTCT 57.438 45.000 5.77 0.00 39.99 2.52
381 422 3.656818 CGAATGATCGCGTCGAAGATTTC 60.657 47.826 10.15 2.61 42.96 2.17
382 423 2.216488 CGAATGATCGCGTCGAAGATTT 59.784 45.455 10.15 0.00 42.96 2.17
383 424 1.781429 CGAATGATCGCGTCGAAGATT 59.219 47.619 10.15 7.22 42.96 2.40
384 425 1.399572 CGAATGATCGCGTCGAAGAT 58.600 50.000 10.15 0.41 42.96 2.40
385 426 2.854772 CGAATGATCGCGTCGAAGA 58.145 52.632 10.15 0.00 42.96 2.87
395 436 3.201290 AGTCATTGTCAGGCGAATGATC 58.799 45.455 0.00 0.00 39.97 2.92
430 471 2.070028 GCCCTTCTGTTTCTTCTCGTC 58.930 52.381 0.00 0.00 0.00 4.20
438 479 4.853924 TTCTCAATTGCCCTTCTGTTTC 57.146 40.909 0.00 0.00 0.00 2.78
442 483 3.120060 CGTCTTTCTCAATTGCCCTTCTG 60.120 47.826 0.00 0.00 0.00 3.02
462 503 0.188834 CCCCCTCTATCCCTCTTCGT 59.811 60.000 0.00 0.00 0.00 3.85
484 525 5.711976 CCTTACACACATCCTTTGATTTCCT 59.288 40.000 0.00 0.00 0.00 3.36
487 528 5.393866 ACCCTTACACACATCCTTTGATTT 58.606 37.500 0.00 0.00 0.00 2.17
490 531 4.141287 CAACCCTTACACACATCCTTTGA 58.859 43.478 0.00 0.00 0.00 2.69
495 536 2.482721 CGTTCAACCCTTACACACATCC 59.517 50.000 0.00 0.00 0.00 3.51
516 557 2.677003 CGGTGGTTGTCGCCATGAC 61.677 63.158 0.00 0.00 46.14 3.06
534 575 3.005897 GGTCCTTTTCTTCTCCCTTTTGC 59.994 47.826 0.00 0.00 0.00 3.68
542 583 4.086706 TGTTCCAGGTCCTTTTCTTCTC 57.913 45.455 0.00 0.00 0.00 2.87
570 611 1.529309 GGAGCCTCAACCCTCCATC 59.471 63.158 0.00 0.00 45.55 3.51
593 634 3.023119 TCTCATGACAGCCTCTCTCTTC 58.977 50.000 0.00 0.00 0.00 2.87
613 654 7.012421 ACACAACTTCTTCTCCTACATTTGTTC 59.988 37.037 0.00 0.00 0.00 3.18
628 669 5.367945 TGTTTCTCCCTACACAACTTCTT 57.632 39.130 0.00 0.00 0.00 2.52
644 685 8.058847 TGCCCTAAGGTATGATTATTTGTTTCT 58.941 33.333 0.00 0.00 34.57 2.52
724 765 1.202114 CCACTATGTGCGCAACCAAAT 59.798 47.619 14.00 3.73 31.34 2.32
793 834 3.239587 TGCCGATTCGACAGTTTATGA 57.760 42.857 7.83 0.00 0.00 2.15
794 835 4.536364 ATTGCCGATTCGACAGTTTATG 57.464 40.909 7.83 0.00 0.00 1.90
796 837 3.372822 GGAATTGCCGATTCGACAGTTTA 59.627 43.478 7.83 0.00 44.21 2.01
814 855 3.677424 GCAGTTTCTGACTCGCTAGGAAT 60.677 47.826 0.66 0.00 36.10 3.01
817 858 1.634702 GCAGTTTCTGACTCGCTAGG 58.365 55.000 0.66 0.00 36.10 3.02
830 871 1.270625 TGAAGGACGATTCGGCAGTTT 60.271 47.619 14.90 4.78 36.10 2.66
831 872 0.320374 TGAAGGACGATTCGGCAGTT 59.680 50.000 14.90 6.35 36.10 3.16
832 873 0.389948 GTGAAGGACGATTCGGCAGT 60.390 55.000 14.90 0.00 36.10 4.40
833 874 0.108615 AGTGAAGGACGATTCGGCAG 60.109 55.000 14.90 0.00 36.10 4.85
834 875 0.108804 GAGTGAAGGACGATTCGGCA 60.109 55.000 14.90 0.00 36.10 5.69
836 877 1.914634 CTGAGTGAAGGACGATTCGG 58.085 55.000 11.29 0.00 31.52 4.30
837 878 1.272781 GCTGAGTGAAGGACGATTCG 58.727 55.000 4.14 4.14 31.52 3.34
838 879 1.646189 GGCTGAGTGAAGGACGATTC 58.354 55.000 0.00 0.00 0.00 2.52
839 880 0.108615 CGGCTGAGTGAAGGACGATT 60.109 55.000 0.00 0.00 0.00 3.34
858 1174 1.141234 GACGACGAAGGGGGATCAC 59.859 63.158 0.00 0.00 0.00 3.06
861 1177 1.757340 GAGGACGACGAAGGGGGAT 60.757 63.158 0.00 0.00 0.00 3.85
862 1178 2.362120 GAGGACGACGAAGGGGGA 60.362 66.667 0.00 0.00 0.00 4.81
908 1232 3.604875 ACACACATAACTTAGGGGACG 57.395 47.619 0.00 0.00 0.00 4.79
922 1246 2.102757 TCTAACGGCCTAACAACACACA 59.897 45.455 0.00 0.00 0.00 3.72
1018 1343 2.819608 GTGCTCCTGCTTGAAATACCAA 59.180 45.455 0.00 0.00 40.48 3.67
1024 1349 2.574006 ATCAGTGCTCCTGCTTGAAA 57.426 45.000 0.00 0.00 41.25 2.69
1029 1354 2.079170 TAGCTATCAGTGCTCCTGCT 57.921 50.000 0.00 0.00 41.25 4.24
1048 1373 2.091499 ACATGACCCATGCCTGAATCAT 60.091 45.455 0.00 0.00 44.80 2.45
1217 1550 4.032960 ACAAGTCTGGCAAATGGTGATA 57.967 40.909 0.00 0.00 0.00 2.15
1219 1552 2.363306 ACAAGTCTGGCAAATGGTGA 57.637 45.000 0.00 0.00 0.00 4.02
1349 1683 0.944386 CTTCCTGAACGTGTTGTGGG 59.056 55.000 0.00 0.00 0.00 4.61
1367 1701 3.199508 CCTTGAGATGGTCTCCATTGACT 59.800 47.826 2.71 0.00 45.26 3.41
1455 1796 1.480954 TGAATCTTGGTAGGAGTCCGC 59.519 52.381 2.76 0.55 0.00 5.54
1557 1908 4.450976 ACAAGATTGTGTTAGTGCTCACA 58.549 39.130 0.00 0.00 40.49 3.58
1612 1963 3.056107 TCTGGCAGTAACATGAGTACCAC 60.056 47.826 15.27 0.00 0.00 4.16
1738 2094 1.352622 TGTGTTGACCCTTCCCAGCT 61.353 55.000 0.00 0.00 0.00 4.24
1810 2168 3.958798 CCTAGGTAGAACTTTCCATCGGA 59.041 47.826 0.00 0.00 0.00 4.55
1881 2239 3.021695 CTCGTTCAGATGGTACCTGGTA 58.978 50.000 14.36 1.49 32.73 3.25
1913 2271 2.022934 GTGGAGTCCTAGGGTAGTTCG 58.977 57.143 11.33 0.00 0.00 3.95
2099 2466 0.518636 CAGGCACCAGTTCGTCAATG 59.481 55.000 0.00 0.00 0.00 2.82
2105 2472 1.079543 CTCCTCAGGCACCAGTTCG 60.080 63.158 0.00 0.00 0.00 3.95
2240 2617 4.815533 TCTTCTTCAGATCCTTGTCTGG 57.184 45.455 4.28 0.00 44.51 3.86
2312 2852 4.761739 TCATCTTACCTCTTTTGTTGCTGG 59.238 41.667 0.00 0.00 0.00 4.85
2313 2853 5.947228 TCATCTTACCTCTTTTGTTGCTG 57.053 39.130 0.00 0.00 0.00 4.41
2314 2854 6.299141 TCTTCATCTTACCTCTTTTGTTGCT 58.701 36.000 0.00 0.00 0.00 3.91
2343 2938 3.053320 GGGAAAGTTCATCATCCCTCCTT 60.053 47.826 2.72 0.00 46.65 3.36
2393 3022 4.447724 ACGCATTATTAAGATGGCAGTACG 59.552 41.667 0.00 0.00 0.00 3.67
2394 3023 5.924475 ACGCATTATTAAGATGGCAGTAC 57.076 39.130 0.00 0.00 0.00 2.73
2395 3024 6.645003 CAGTACGCATTATTAAGATGGCAGTA 59.355 38.462 0.00 0.00 0.00 2.74
2396 3025 5.466728 CAGTACGCATTATTAAGATGGCAGT 59.533 40.000 0.00 0.00 0.00 4.40
2397 3026 5.615544 GCAGTACGCATTATTAAGATGGCAG 60.616 44.000 0.00 0.00 41.79 4.85
2398 3027 4.213270 GCAGTACGCATTATTAAGATGGCA 59.787 41.667 0.00 0.00 41.79 4.92
2399 3028 4.378459 GGCAGTACGCATTATTAAGATGGC 60.378 45.833 10.92 0.00 45.17 4.40
2400 3029 4.754618 TGGCAGTACGCATTATTAAGATGG 59.245 41.667 10.92 0.00 45.17 3.51
2401 3030 5.922739 TGGCAGTACGCATTATTAAGATG 57.077 39.130 10.92 0.00 45.17 2.90
2402 3031 7.228507 TCAAATGGCAGTACGCATTATTAAGAT 59.771 33.333 10.92 0.00 45.17 2.40
2403 3032 6.540551 TCAAATGGCAGTACGCATTATTAAGA 59.459 34.615 10.92 7.62 45.17 2.10
2404 3033 6.724263 TCAAATGGCAGTACGCATTATTAAG 58.276 36.000 10.92 6.12 45.17 1.85
2405 3034 6.685527 TCAAATGGCAGTACGCATTATTAA 57.314 33.333 10.92 0.00 45.17 1.40
2406 3035 6.875948 ATCAAATGGCAGTACGCATTATTA 57.124 33.333 10.92 0.00 45.17 0.98
2407 3036 5.772825 ATCAAATGGCAGTACGCATTATT 57.227 34.783 10.92 6.28 45.17 1.40
2408 3037 5.997746 ACTATCAAATGGCAGTACGCATTAT 59.002 36.000 10.92 1.52 45.17 1.28
2409 3038 5.364778 ACTATCAAATGGCAGTACGCATTA 58.635 37.500 10.92 0.00 45.17 1.90
2410 3039 4.199310 ACTATCAAATGGCAGTACGCATT 58.801 39.130 10.92 6.73 45.17 3.56
2411 3040 3.808728 ACTATCAAATGGCAGTACGCAT 58.191 40.909 10.92 2.03 45.17 4.73
2412 3041 3.260475 ACTATCAAATGGCAGTACGCA 57.740 42.857 10.92 0.09 45.17 5.24
2413 3042 3.184581 GCTACTATCAAATGGCAGTACGC 59.815 47.826 0.00 1.72 41.28 4.42
2414 3043 4.621991 AGCTACTATCAAATGGCAGTACG 58.378 43.478 0.00 0.00 0.00 3.67
2438 3067 4.128643 ACGAAACAAATTACGGTTCCTCA 58.871 39.130 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.