Multiple sequence alignment - TraesCS5A01G139900

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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 TraesCS5A01G139900 chr5A 100.000 3032 0 0 1 3032 312234324 312231293 0.000000e+00 5600.0
1 TraesCS5A01G139900 chr5D 94.722 1724 58 13 562 2276 242014909 242013210 0.000000e+00 2649.0
2 TraesCS5A01G139900 chr5D 89.157 498 43 8 2545 3032 242012847 242012351 7.190000e-171 610.0
3 TraesCS5A01G139900 chr5D 91.339 254 10 2 4 256 242015960 242015718 1.350000e-88 337.0
4 TraesCS5A01G139900 chr5D 86.641 262 19 8 275 534 242015375 242015128 2.980000e-70 276.0
5 TraesCS5A01G139900 chr5B 92.810 1683 79 19 610 2277 257003183 257001528 0.000000e+00 2399.0
6 TraesCS5A01G139900 chr5B 89.022 501 44 7 2539 3032 257001251 257000755 7.190000e-171 610.0
7 TraesCS5A01G139900 chr5B 83.333 462 21 20 114 564 257003882 257003466 2.850000e-100 375.0
8 TraesCS5A01G139900 chr5B 91.597 119 7 1 7 125 257004028 257003913 8.700000e-36 161.0
9 TraesCS5A01G139900 chr1B 75.723 346 58 22 1033 1359 551233744 551233406 1.880000e-32 150.0
10 TraesCS5A01G139900 chr1B 75.391 256 45 14 1033 1282 551230600 551230357 1.150000e-19 108.0
11 TraesCS5A01G139900 chr1B 74.532 267 49 14 1110 1359 39564954 39565218 6.920000e-17 99.0
12 TraesCS5A01G139900 chr1A 75.660 341 61 19 1033 1359 505483968 505483636 1.880000e-32 150.0
13 TraesCS5A01G139900 chr1D 75.072 345 59 22 1033 1359 409529037 409528702 5.270000e-28 135.0
14 TraesCS5A01G139900 chr3B 75.269 186 33 9 1110 1284 10181196 10181379 3.240000e-10 76.8
15 TraesCS5A01G139900 chr3D 77.311 119 21 5 1247 1359 435444234 435444352 7.020000e-07 65.8


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 TraesCS5A01G139900 chr5A 312231293 312234324 3031 True 5600.00 5600 100.00000 1 3032 1 chr5A.!!$R1 3031
1 TraesCS5A01G139900 chr5D 242012351 242015960 3609 True 968.00 2649 90.46475 4 3032 4 chr5D.!!$R1 3028
2 TraesCS5A01G139900 chr5B 257000755 257004028 3273 True 886.25 2399 89.19050 7 3032 4 chr5B.!!$R1 3025

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
119 120 0.541063 TCCACCCGTACAGAGAAGCA 60.541 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2731 0.519961 GCGCGGGAACAGTAAAACAT 59.48 50.0 8.83 0.0 0.0 2.71 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
103 104 3.235481 TCCGACCACGCCTTTCCA 61.235 61.111 0.00 0.00 38.29 3.53
119 120 0.541063 TCCACCCGTACAGAGAAGCA 60.541 55.000 0.00 0.00 0.00 3.91
222 266 1.668419 AGAAACATATGGACGCCAGC 58.332 50.000 7.80 0.00 36.75 4.85
241 285 5.631096 GCCAGCTTTCACTAAAATCTTGTTC 59.369 40.000 0.00 0.00 0.00 3.18
312 680 7.475015 TCTTGTTCACTTGTCTCAGAAAAATG 58.525 34.615 0.00 0.00 0.00 2.32
354 723 8.015658 CACTTTCCTAAAAACCGAATAGTGAAG 58.984 37.037 0.00 0.00 32.48 3.02
400 769 8.846943 AAAACAAAATTTGAGGGTCATATTCC 57.153 30.769 13.19 0.00 28.96 3.01
476 856 1.653094 ATTACACGCCATTGCCACCG 61.653 55.000 0.00 0.00 0.00 4.94
503 883 3.038280 TCATGTCCATATTCGTGGTCCT 58.962 45.455 0.00 0.00 40.27 3.85
504 884 4.219919 TCATGTCCATATTCGTGGTCCTA 58.780 43.478 0.00 0.00 40.27 2.94
505 885 4.651962 TCATGTCCATATTCGTGGTCCTAA 59.348 41.667 0.00 0.00 40.27 2.69
534 925 5.751243 TCACGATCAATCTTGACGATCTA 57.249 39.130 16.25 2.95 40.49 1.98
535 926 6.131544 TCACGATCAATCTTGACGATCTAA 57.868 37.500 16.25 0.00 40.49 2.10
536 927 6.202226 TCACGATCAATCTTGACGATCTAAG 58.798 40.000 16.25 0.00 40.49 2.18
537 928 6.038271 TCACGATCAATCTTGACGATCTAAGA 59.962 38.462 16.25 6.45 40.49 2.10
538 929 6.693113 CACGATCAATCTTGACGATCTAAGAA 59.307 38.462 16.25 0.00 40.49 2.52
539 930 7.220875 CACGATCAATCTTGACGATCTAAGAAA 59.779 37.037 16.25 0.32 40.49 2.52
540 931 7.759886 ACGATCAATCTTGACGATCTAAGAAAA 59.240 33.333 16.25 0.07 40.49 2.29
541 932 8.053072 CGATCAATCTTGACGATCTAAGAAAAC 58.947 37.037 7.66 0.00 40.49 2.43
542 933 7.596749 TCAATCTTGACGATCTAAGAAAACC 57.403 36.000 7.66 0.00 36.59 3.27
543 934 6.594159 TCAATCTTGACGATCTAAGAAAACCC 59.406 38.462 7.66 0.00 36.59 4.11
544 935 5.740290 TCTTGACGATCTAAGAAAACCCT 57.260 39.130 0.00 0.00 30.49 4.34
548 939 4.527038 TGACGATCTAAGAAAACCCTCACT 59.473 41.667 0.00 0.00 0.00 3.41
555 946 9.232473 GATCTAAGAAAACCCTCACTGTTTATT 57.768 33.333 0.00 0.00 34.97 1.40
570 1173 5.842328 ACTGTTTATTATCGATCCCCCACTA 59.158 40.000 0.00 0.00 0.00 2.74
597 1200 3.256136 GGAACGAGGGACGATATCTCAAT 59.744 47.826 0.34 0.00 45.77 2.57
598 1201 4.262079 GGAACGAGGGACGATATCTCAATT 60.262 45.833 0.34 0.00 45.77 2.32
599 1202 4.506886 ACGAGGGACGATATCTCAATTC 57.493 45.455 0.34 0.00 45.77 2.17
600 1203 4.145807 ACGAGGGACGATATCTCAATTCT 58.854 43.478 0.34 0.00 45.77 2.40
601 1204 4.216687 ACGAGGGACGATATCTCAATTCTC 59.783 45.833 0.34 0.51 45.77 2.87
602 1205 4.216472 CGAGGGACGATATCTCAATTCTCA 59.784 45.833 0.34 0.00 45.77 3.27
603 1206 5.278512 CGAGGGACGATATCTCAATTCTCAA 60.279 44.000 0.34 0.00 45.77 3.02
617 1252 0.678950 TCTCAACCTGCGATGTGACA 59.321 50.000 0.00 0.00 0.00 3.58
620 1255 1.805943 TCAACCTGCGATGTGACATTG 59.194 47.619 8.46 8.46 0.00 2.82
635 1270 3.433274 TGACATTGATCTTGTTCGTGCTC 59.567 43.478 0.00 0.00 0.00 4.26
640 1275 2.224042 TGATCTTGTTCGTGCTCTGTGT 60.224 45.455 0.00 0.00 0.00 3.72
719 1355 6.766429 TGATGAGGCGTCTAGTCTAAGTATA 58.234 40.000 8.06 0.00 33.03 1.47
721 1357 7.883833 TGATGAGGCGTCTAGTCTAAGTATATT 59.116 37.037 8.06 0.00 33.03 1.28
722 1358 8.638629 ATGAGGCGTCTAGTCTAAGTATATTT 57.361 34.615 8.06 0.00 33.03 1.40
723 1359 8.097078 TGAGGCGTCTAGTCTAAGTATATTTC 57.903 38.462 8.06 0.00 33.03 2.17
724 1360 7.174599 TGAGGCGTCTAGTCTAAGTATATTTCC 59.825 40.741 8.06 0.00 33.03 3.13
725 1361 7.002879 AGGCGTCTAGTCTAAGTATATTTCCA 58.997 38.462 0.00 0.00 29.53 3.53
726 1362 7.670559 AGGCGTCTAGTCTAAGTATATTTCCAT 59.329 37.037 0.00 0.00 29.53 3.41
727 1363 8.954350 GGCGTCTAGTCTAAGTATATTTCCATA 58.046 37.037 0.00 0.00 0.00 2.74
728 1364 9.991388 GCGTCTAGTCTAAGTATATTTCCATAG 57.009 37.037 0.00 0.00 0.00 2.23
822 1462 2.525105 AATGGATTGCTTAACCCCGT 57.475 45.000 0.00 0.00 0.00 5.28
852 1492 1.814394 TCTTGCATTGCATCCACAGTC 59.186 47.619 12.95 0.00 38.76 3.51
865 1505 2.170397 TCCACAGTCAAGCAACAGAGAA 59.830 45.455 0.00 0.00 0.00 2.87
871 1511 2.225255 GTCAAGCAACAGAGAAGAAGCC 59.775 50.000 0.00 0.00 0.00 4.35
874 1514 1.003003 AGCAACAGAGAAGAAGCCTCC 59.997 52.381 0.00 0.00 0.00 4.30
910 1550 2.901051 ATCGTCGGGGACATTCGCAC 62.901 60.000 0.00 0.00 32.09 5.34
969 1609 2.017782 CTGAGGTGACGAAGCTAGCTA 58.982 52.381 19.70 0.00 36.52 3.32
971 1611 0.733729 AGGTGACGAAGCTAGCTACG 59.266 55.000 19.70 10.20 33.90 3.51
973 1613 1.667724 GGTGACGAAGCTAGCTACGTA 59.332 52.381 19.70 0.88 39.04 3.57
974 1614 2.538535 GGTGACGAAGCTAGCTACGTAC 60.539 54.545 19.70 13.19 39.04 3.67
975 1615 2.094894 GTGACGAAGCTAGCTACGTACA 59.905 50.000 19.70 11.95 39.04 2.90
976 1616 2.941064 TGACGAAGCTAGCTACGTACAT 59.059 45.455 19.70 0.00 39.04 2.29
978 1618 3.692576 ACGAAGCTAGCTACGTACATTG 58.307 45.455 19.70 6.85 37.22 2.82
980 1620 3.242969 CGAAGCTAGCTACGTACATTGGA 60.243 47.826 19.70 0.00 0.00 3.53
981 1621 4.556898 CGAAGCTAGCTACGTACATTGGAT 60.557 45.833 19.70 0.00 0.00 3.41
982 1622 4.506886 AGCTAGCTACGTACATTGGATC 57.493 45.455 17.69 0.00 0.00 3.36
983 1623 3.058155 AGCTAGCTACGTACATTGGATCG 60.058 47.826 17.69 0.00 0.00 3.69
984 1624 2.795175 AGCTACGTACATTGGATCGG 57.205 50.000 0.00 0.00 0.00 4.18
985 1625 2.304092 AGCTACGTACATTGGATCGGA 58.696 47.619 0.00 0.00 0.00 4.55
986 1626 2.691526 AGCTACGTACATTGGATCGGAA 59.308 45.455 0.00 0.00 0.00 4.30
987 1627 2.793232 GCTACGTACATTGGATCGGAAC 59.207 50.000 0.00 0.00 0.00 3.62
1012 1652 0.842635 CAAGAAGATGGAGGGGGAGG 59.157 60.000 0.00 0.00 0.00 4.30
1016 1656 3.237741 GATGGAGGGGGAGGCGAG 61.238 72.222 0.00 0.00 0.00 5.03
1431 2071 1.626654 CCATTGTGTCCGACTCGTGC 61.627 60.000 0.00 0.00 0.00 5.34
1758 2407 1.587933 GCCAGACGAACGAGACCTCT 61.588 60.000 0.14 0.00 0.00 3.69
1932 2581 2.125512 CACCCGTGCCTCTACTGC 60.126 66.667 0.00 0.00 0.00 4.40
2082 2731 1.441738 CATGCGTTCCTCATGTGTCA 58.558 50.000 0.00 0.00 37.22 3.58
2097 2746 5.240623 TCATGTGTCATGTTTTACTGTTCCC 59.759 40.000 9.13 0.00 0.00 3.97
2211 2860 5.393962 GGATTTGTTATGACTCACTTGCAC 58.606 41.667 0.00 0.00 0.00 4.57
2217 2866 5.639082 TGTTATGACTCACTTGCACATACTG 59.361 40.000 0.00 0.00 0.00 2.74
2219 2868 4.541973 TGACTCACTTGCACATACTGAT 57.458 40.909 0.00 0.00 0.00 2.90
2269 2918 6.545504 TGAAATCTTCACTTACAACTCTGC 57.454 37.500 0.00 0.00 34.08 4.26
2273 2922 5.036117 TCTTCACTTACAACTCTGCCTTT 57.964 39.130 0.00 0.00 0.00 3.11
2277 2926 3.316308 CACTTACAACTCTGCCTTTGCTT 59.684 43.478 0.00 0.00 38.71 3.91
2278 2927 3.565902 ACTTACAACTCTGCCTTTGCTTC 59.434 43.478 0.00 0.00 38.71 3.86
2279 2928 2.355010 ACAACTCTGCCTTTGCTTCT 57.645 45.000 0.00 0.00 38.71 2.85
2280 2929 2.659428 ACAACTCTGCCTTTGCTTCTT 58.341 42.857 0.00 0.00 38.71 2.52
2281 2930 2.360165 ACAACTCTGCCTTTGCTTCTTG 59.640 45.455 0.00 0.00 38.71 3.02
2282 2931 2.355010 ACTCTGCCTTTGCTTCTTGT 57.645 45.000 0.00 0.00 38.71 3.16
2283 2932 3.492102 ACTCTGCCTTTGCTTCTTGTA 57.508 42.857 0.00 0.00 38.71 2.41
2284 2933 4.026356 ACTCTGCCTTTGCTTCTTGTAT 57.974 40.909 0.00 0.00 38.71 2.29
2285 2934 3.755378 ACTCTGCCTTTGCTTCTTGTATG 59.245 43.478 0.00 0.00 38.71 2.39
2286 2935 3.754965 TCTGCCTTTGCTTCTTGTATGT 58.245 40.909 0.00 0.00 38.71 2.29
2287 2936 4.144297 TCTGCCTTTGCTTCTTGTATGTT 58.856 39.130 0.00 0.00 38.71 2.71
2288 2937 4.584325 TCTGCCTTTGCTTCTTGTATGTTT 59.416 37.500 0.00 0.00 38.71 2.83
2289 2938 5.068987 TCTGCCTTTGCTTCTTGTATGTTTT 59.931 36.000 0.00 0.00 38.71 2.43
2290 2939 5.669477 TGCCTTTGCTTCTTGTATGTTTTT 58.331 33.333 0.00 0.00 38.71 1.94
2316 2965 9.624697 TTTCTTGTTTTGCTTATATGTGATGAC 57.375 29.630 0.00 0.00 0.00 3.06
2317 2966 8.565896 TCTTGTTTTGCTTATATGTGATGACT 57.434 30.769 0.00 0.00 0.00 3.41
2318 2967 9.013229 TCTTGTTTTGCTTATATGTGATGACTT 57.987 29.630 0.00 0.00 0.00 3.01
2319 2968 9.630098 CTTGTTTTGCTTATATGTGATGACTTT 57.370 29.630 0.00 0.00 0.00 2.66
2352 3001 5.444744 AAATGTGGTGTGGGCTTAGTATA 57.555 39.130 0.00 0.00 0.00 1.47
2358 3007 4.406326 TGGTGTGGGCTTAGTATATCGAAA 59.594 41.667 0.00 0.00 0.00 3.46
2362 3011 4.448060 GTGGGCTTAGTATATCGAAAGTGC 59.552 45.833 0.00 0.00 0.00 4.40
2367 3016 6.090088 GGCTTAGTATATCGAAAGTGCTCATG 59.910 42.308 0.00 0.00 0.00 3.07
2374 3023 5.786401 ATCGAAAGTGCTCATGAGTTTAC 57.214 39.130 23.38 18.49 0.00 2.01
2394 3043 2.480037 ACAGTGTGCATGTGTACATTCG 59.520 45.455 7.18 2.53 42.31 3.34
2399 3048 5.641636 AGTGTGCATGTGTACATTCGAAATA 59.358 36.000 0.00 0.00 42.31 1.40
2404 3053 7.696035 GTGCATGTGTACATTCGAAATAATGAA 59.304 33.333 0.00 0.00 38.84 2.57
2436 3085 9.993454 ATGCATATATGTAAGCATCTATCGATT 57.007 29.630 14.14 0.00 40.19 3.34
2522 3271 4.138290 TGCCGTTTTCTTCATCCTTGTTA 58.862 39.130 0.00 0.00 0.00 2.41
2527 3276 6.959311 CCGTTTTCTTCATCCTTGTTAATACG 59.041 38.462 0.00 0.00 0.00 3.06
2531 3280 7.827819 TTCTTCATCCTTGTTAATACGTCAG 57.172 36.000 0.00 0.00 0.00 3.51
2543 3334 4.450082 AATACGTCAGTGCATGTCTACA 57.550 40.909 0.00 0.00 0.00 2.74
2557 3348 8.289618 GTGCATGTCTACAAACTCTTTTAATCA 58.710 33.333 0.00 0.00 0.00 2.57
2578 3369 7.739498 ATCATTTTCCGTTTTAGTGTACAGT 57.261 32.000 8.55 8.55 0.00 3.55
2665 3461 4.870123 TCCAGGTGGAATGAACATTTTG 57.130 40.909 0.00 0.00 42.18 2.44
2825 3623 9.683069 ACAATTTCTCTAACATGTGAACATTTC 57.317 29.630 0.00 0.00 33.61 2.17
2831 3629 9.513906 TCTCTAACATGTGAACATTTCCATAAA 57.486 29.630 0.00 0.00 33.61 1.40
2854 3652 6.588719 ATGCTGTGCCTCTGTTTTTAAATA 57.411 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.726631 GACGAGCGACAGAGGAGCG 62.727 68.421 0.00 0.00 35.78 5.03
49 50 2.101380 GACGAGCGACAGAGGAGC 59.899 66.667 0.00 0.00 0.00 4.70
52 53 2.299294 GACTCGACGAGCGACAGAGG 62.299 65.000 24.38 0.00 45.59 3.69
53 54 1.059681 GACTCGACGAGCGACAGAG 59.940 63.158 24.38 0.00 45.59 3.35
54 55 2.727684 CGACTCGACGAGCGACAGA 61.728 63.158 26.53 0.00 45.59 3.41
55 56 2.276120 CGACTCGACGAGCGACAG 60.276 66.667 26.53 11.76 45.59 3.51
103 104 1.585006 CGTGCTTCTCTGTACGGGT 59.415 57.895 0.85 0.00 41.15 5.28
222 266 6.490040 TGAGGGGAACAAGATTTTAGTGAAAG 59.510 38.462 0.00 0.00 0.00 2.62
343 712 4.090066 CCGTGAACAAGACTTCACTATTCG 59.910 45.833 9.68 0.00 45.40 3.34
428 799 0.617249 CTTCCAGGGGAGCTCTCTGT 60.617 60.000 24.90 9.32 31.21 3.41
476 856 5.299279 ACCACGAATATGGACATGAATTTCC 59.701 40.000 0.00 0.00 43.02 3.13
504 884 9.476202 TCGTCAAGATTGATCGTGATAATTATT 57.524 29.630 11.70 0.00 44.67 1.40
505 885 9.645059 ATCGTCAAGATTGATCGTGATAATTAT 57.355 29.630 11.70 0.00 44.67 1.28
534 925 7.881232 TCGATAATAAACAGTGAGGGTTTTCTT 59.119 33.333 0.00 0.00 39.12 2.52
535 926 7.391620 TCGATAATAAACAGTGAGGGTTTTCT 58.608 34.615 0.00 0.00 39.12 2.52
536 927 7.605410 TCGATAATAAACAGTGAGGGTTTTC 57.395 36.000 0.00 0.00 39.12 2.29
537 928 7.282450 GGATCGATAATAAACAGTGAGGGTTTT 59.718 37.037 0.00 0.00 39.12 2.43
538 929 6.766467 GGATCGATAATAAACAGTGAGGGTTT 59.234 38.462 0.00 0.00 41.11 3.27
539 930 6.289064 GGATCGATAATAAACAGTGAGGGTT 58.711 40.000 0.00 0.00 0.00 4.11
540 931 5.221661 GGGATCGATAATAAACAGTGAGGGT 60.222 44.000 0.00 0.00 0.00 4.34
541 932 5.238583 GGGATCGATAATAAACAGTGAGGG 58.761 45.833 0.00 0.00 0.00 4.30
542 933 5.238583 GGGGATCGATAATAAACAGTGAGG 58.761 45.833 0.00 0.00 0.00 3.86
543 934 5.221641 TGGGGGATCGATAATAAACAGTGAG 60.222 44.000 0.00 0.00 0.00 3.51
544 935 4.656575 TGGGGGATCGATAATAAACAGTGA 59.343 41.667 0.00 0.00 0.00 3.41
548 939 6.079336 TCTAGTGGGGGATCGATAATAAACA 58.921 40.000 0.00 0.00 0.00 2.83
555 946 3.141460 TCCTTTCTAGTGGGGGATCGATA 59.859 47.826 0.00 0.00 0.00 2.92
570 1173 1.558233 ATCGTCCCTCGTTCCTTTCT 58.442 50.000 0.00 0.00 40.80 2.52
597 1200 1.069978 TGTCACATCGCAGGTTGAGAA 59.930 47.619 0.00 0.00 28.16 2.87
598 1201 0.678950 TGTCACATCGCAGGTTGAGA 59.321 50.000 0.00 0.00 0.00 3.27
599 1202 1.730501 ATGTCACATCGCAGGTTGAG 58.269 50.000 0.00 0.00 0.00 3.02
600 1203 1.805943 CAATGTCACATCGCAGGTTGA 59.194 47.619 0.00 0.00 0.00 3.18
601 1204 1.805943 TCAATGTCACATCGCAGGTTG 59.194 47.619 0.00 0.00 0.00 3.77
602 1205 2.183478 TCAATGTCACATCGCAGGTT 57.817 45.000 0.00 0.00 0.00 3.50
603 1206 2.093288 AGATCAATGTCACATCGCAGGT 60.093 45.455 0.00 0.00 0.00 4.00
617 1252 3.434641 CACAGAGCACGAACAAGATCAAT 59.565 43.478 0.00 0.00 0.00 2.57
620 1255 2.408050 ACACAGAGCACGAACAAGATC 58.592 47.619 0.00 0.00 0.00 2.75
635 1270 4.506288 TGCGAATCATTAATCGGTACACAG 59.494 41.667 0.00 0.00 39.38 3.66
640 1275 5.502706 CGGTTTTGCGAATCATTAATCGGTA 60.503 40.000 0.00 0.00 39.38 4.02
721 1357 8.721479 AGTACATCCTACACTACTACTATGGAA 58.279 37.037 0.00 0.00 0.00 3.53
722 1358 8.272659 AGTACATCCTACACTACTACTATGGA 57.727 38.462 0.00 0.00 0.00 3.41
723 1359 9.434420 GTAGTACATCCTACACTACTACTATGG 57.566 40.741 0.00 0.00 40.84 2.74
724 1360 9.434420 GGTAGTACATCCTACACTACTACTATG 57.566 40.741 2.06 0.00 42.69 2.23
725 1361 9.163894 TGGTAGTACATCCTACACTACTACTAT 57.836 37.037 2.06 0.00 42.69 2.12
726 1362 8.553085 TGGTAGTACATCCTACACTACTACTA 57.447 38.462 2.06 5.25 42.69 1.82
727 1363 7.346698 TCTGGTAGTACATCCTACACTACTACT 59.653 40.741 2.06 0.00 42.69 2.57
728 1364 7.440856 GTCTGGTAGTACATCCTACACTACTAC 59.559 44.444 2.06 0.00 42.69 2.73
798 1438 3.430790 GGGGTTAAGCAATCCATTTCTGC 60.431 47.826 7.03 0.00 36.55 4.26
852 1492 2.483491 GAGGCTTCTTCTCTGTTGCTTG 59.517 50.000 0.00 0.00 0.00 4.01
865 1505 4.649674 TGAACTCGTTATATGGAGGCTTCT 59.350 41.667 0.00 0.00 34.58 2.85
871 1511 4.846677 CGATCGTGAACTCGTTATATGGAG 59.153 45.833 7.03 0.35 36.36 3.86
910 1550 1.086067 CAGGCTACCGTGTGCAGATG 61.086 60.000 0.00 0.00 0.00 2.90
969 1609 2.028839 TGTGTTCCGATCCAATGTACGT 60.029 45.455 0.00 0.00 0.00 3.57
971 1611 2.347452 CGTGTGTTCCGATCCAATGTAC 59.653 50.000 0.00 0.00 0.00 2.90
973 1613 1.438651 CGTGTGTTCCGATCCAATGT 58.561 50.000 0.00 0.00 0.00 2.71
974 1614 0.096976 GCGTGTGTTCCGATCCAATG 59.903 55.000 0.00 0.00 0.00 2.82
975 1615 0.321210 TGCGTGTGTTCCGATCCAAT 60.321 50.000 0.00 0.00 0.00 3.16
976 1616 0.533085 TTGCGTGTGTTCCGATCCAA 60.533 50.000 0.00 0.00 0.00 3.53
978 1618 0.669318 TCTTGCGTGTGTTCCGATCC 60.669 55.000 0.00 0.00 0.00 3.36
980 1620 1.148310 CTTCTTGCGTGTGTTCCGAT 58.852 50.000 0.00 0.00 0.00 4.18
981 1621 0.103390 TCTTCTTGCGTGTGTTCCGA 59.897 50.000 0.00 0.00 0.00 4.55
982 1622 1.136252 CATCTTCTTGCGTGTGTTCCG 60.136 52.381 0.00 0.00 0.00 4.30
983 1623 1.197721 CCATCTTCTTGCGTGTGTTCC 59.802 52.381 0.00 0.00 0.00 3.62
984 1624 2.143122 TCCATCTTCTTGCGTGTGTTC 58.857 47.619 0.00 0.00 0.00 3.18
985 1625 2.146342 CTCCATCTTCTTGCGTGTGTT 58.854 47.619 0.00 0.00 0.00 3.32
986 1626 1.609061 CCTCCATCTTCTTGCGTGTGT 60.609 52.381 0.00 0.00 0.00 3.72
987 1627 1.081892 CCTCCATCTTCTTGCGTGTG 58.918 55.000 0.00 0.00 0.00 3.82
1329 1969 2.047274 AAGTCGGTGGGCACGATG 60.047 61.111 0.00 0.00 42.82 3.84
1338 1978 2.069273 GTGATGAGGTTGAAGTCGGTG 58.931 52.381 0.00 0.00 0.00 4.94
1923 2572 2.202623 GCGTCGGTGCAGTAGAGG 60.203 66.667 0.00 0.00 34.15 3.69
2082 2731 0.519961 GCGCGGGAACAGTAAAACAT 59.480 50.000 8.83 0.00 0.00 2.71
2211 2860 8.599055 AGCTACAATAATGACACATCAGTATG 57.401 34.615 0.00 0.00 43.56 2.39
2217 2866 8.454106 ACTTTGAAGCTACAATAATGACACATC 58.546 33.333 0.00 0.00 0.00 3.06
2219 2868 7.443879 TGACTTTGAAGCTACAATAATGACACA 59.556 33.333 0.00 0.00 0.00 3.72
2290 2939 9.624697 GTCATCACATATAAGCAAAACAAGAAA 57.375 29.630 0.00 0.00 0.00 2.52
2291 2940 9.013229 AGTCATCACATATAAGCAAAACAAGAA 57.987 29.630 0.00 0.00 0.00 2.52
2292 2941 8.565896 AGTCATCACATATAAGCAAAACAAGA 57.434 30.769 0.00 0.00 0.00 3.02
2293 2942 9.630098 AAAGTCATCACATATAAGCAAAACAAG 57.370 29.630 0.00 0.00 0.00 3.16
2313 2962 9.258826 CACCACATTTTGAAATTGATAAAGTCA 57.741 29.630 6.79 0.00 34.25 3.41
2314 2963 9.260002 ACACCACATTTTGAAATTGATAAAGTC 57.740 29.630 6.79 0.00 0.00 3.01
2315 2964 9.044150 CACACCACATTTTGAAATTGATAAAGT 57.956 29.630 6.79 0.00 0.00 2.66
2316 2965 8.497554 CCACACCACATTTTGAAATTGATAAAG 58.502 33.333 6.79 0.00 0.00 1.85
2317 2966 7.443575 CCCACACCACATTTTGAAATTGATAAA 59.556 33.333 6.79 0.00 0.00 1.40
2318 2967 6.933521 CCCACACCACATTTTGAAATTGATAA 59.066 34.615 6.79 0.00 0.00 1.75
2319 2968 6.462500 CCCACACCACATTTTGAAATTGATA 58.538 36.000 6.79 0.00 0.00 2.15
2320 2969 5.307204 CCCACACCACATTTTGAAATTGAT 58.693 37.500 6.79 0.00 0.00 2.57
2321 2970 4.701765 CCCACACCACATTTTGAAATTGA 58.298 39.130 6.79 0.00 0.00 2.57
2331 2980 5.621193 GATATACTAAGCCCACACCACATT 58.379 41.667 0.00 0.00 0.00 2.71
2337 2986 5.462398 CACTTTCGATATACTAAGCCCACAC 59.538 44.000 0.00 0.00 0.00 3.82
2352 3001 5.237815 TGTAAACTCATGAGCACTTTCGAT 58.762 37.500 22.83 0.00 0.00 3.59
2358 3007 4.060900 CACACTGTAAACTCATGAGCACT 58.939 43.478 22.83 9.60 0.00 4.40
2362 3011 4.453478 ACATGCACACTGTAAACTCATGAG 59.547 41.667 21.37 21.37 35.25 2.90
2367 3016 4.509970 TGTACACATGCACACTGTAAACTC 59.490 41.667 0.00 0.00 0.00 3.01
2374 3023 2.736192 TCGAATGTACACATGCACACTG 59.264 45.455 0.00 0.00 36.56 3.66
2486 3208 4.385358 AAACGGCAAGAAACAAAGACAT 57.615 36.364 0.00 0.00 0.00 3.06
2493 3215 4.499019 GGATGAAGAAAACGGCAAGAAACA 60.499 41.667 0.00 0.00 0.00 2.83
2495 3217 3.888930 AGGATGAAGAAAACGGCAAGAAA 59.111 39.130 0.00 0.00 0.00 2.52
2522 3271 4.450082 TGTAGACATGCACTGACGTATT 57.550 40.909 0.00 0.00 0.00 1.89
2527 3276 4.310769 AGAGTTTGTAGACATGCACTGAC 58.689 43.478 0.00 0.00 0.00 3.51
2531 3280 8.289618 TGATTAAAAGAGTTTGTAGACATGCAC 58.710 33.333 0.00 0.00 0.00 4.57
2557 3348 7.739498 ATCACTGTACACTAAAACGGAAAAT 57.261 32.000 0.00 0.00 0.00 1.82
2563 3354 9.150653 GTGTAAAAATCACTGTACACTAAAACG 57.849 33.333 0.00 0.00 41.90 3.60
2789 3587 8.767085 CATGTTAGAGAAATTGTTTGTGCATTT 58.233 29.630 0.00 0.00 0.00 2.32
2825 3623 2.372264 ACAGAGGCACAGCATTTATGG 58.628 47.619 0.00 0.00 0.00 2.74
2831 3629 4.935352 TTTAAAAACAGAGGCACAGCAT 57.065 36.364 0.00 0.00 0.00 3.79
2834 3632 8.730680 AGTATGTATTTAAAAACAGAGGCACAG 58.269 33.333 0.00 0.00 0.00 3.66
2962 3761 4.413495 ACCATCCACGAAAATGTTTACG 57.587 40.909 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.