Multiple sequence alignment - TraesCS7D01G460300

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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 TraesCS7D01G460300 chr7D 100.000 3186 0 0 1 3186 576956894 576953709 0.000000e+00 5884.0
1 TraesCS7D01G460300 chr7A 91.994 1986 82 24 442 2400 668998302 669000237 0.000000e+00 2715.0
2 TraesCS7D01G460300 chr7A 90.152 1117 74 21 1327 2424 80594767 80595866 0.000000e+00 1421.0
3 TraesCS7D01G460300 chr7A 88.974 780 52 16 552 1323 80593965 80594718 0.000000e+00 933.0
4 TraesCS7D01G460300 chr7A 91.908 346 18 4 2055 2400 669003852 669004187 2.880000e-130 475.0
5 TraesCS7D01G460300 chr7B 94.793 1229 39 10 1321 2546 639793474 639794680 0.000000e+00 1892.0
6 TraesCS7D01G460300 chr7B 90.719 1336 66 34 1 1323 639792145 639793435 0.000000e+00 1727.0
7 TraesCS7D01G460300 chr7B 95.857 1062 29 7 1321 2376 639807719 639808771 0.000000e+00 1703.0
8 TraesCS7D01G460300 chr7B 95.847 313 9 2 1014 1323 639807369 639807680 1.320000e-138 503.0
9 TraesCS7D01G460300 chr7B 92.614 352 20 5 2836 3186 639795213 639795559 4.740000e-138 501.0
10 TraesCS7D01G460300 chr7B 90.157 254 20 4 2550 2802 639794968 639795217 3.060000e-85 326.0
11 TraesCS7D01G460300 chr7B 93.981 216 7 5 2962 3175 639810792 639811003 3.960000e-84 322.0
12 TraesCS7D01G460300 chr4A 90.909 44 4 0 350 393 553454285 553454242 3.430000e-05 60.2


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 TraesCS7D01G460300 chr7D 576953709 576956894 3185 True 5884.000000 5884 100.000000 1 3186 1 chr7D.!!$R1 3185
1 TraesCS7D01G460300 chr7A 668998302 669004187 5885 False 1595.000000 2715 91.951000 442 2400 2 chr7A.!!$F2 1958
2 TraesCS7D01G460300 chr7A 80593965 80595866 1901 False 1177.000000 1421 89.563000 552 2424 2 chr7A.!!$F1 1872
3 TraesCS7D01G460300 chr7B 639792145 639795559 3414 False 1111.500000 1892 92.070750 1 3186 4 chr7B.!!$F1 3185
4 TraesCS7D01G460300 chr7B 639807369 639811003 3634 False 842.666667 1703 95.228333 1014 3175 3 chr7B.!!$F2 2161

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
80 81 0.163788 CGCTCGAACGTGCAGAAAAT 59.836 50.0 18.32 0.0 34.68 1.82 F
939 958 0.319040 TCATATTGCTCTCTCCGCGC 60.319 55.0 0.00 0.0 0.00 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 1898 0.445436 GGACAGTTCTTGCAGCATCG 59.555 55.0 0.0 0.0 0.0 3.84 R
2676 7731 0.179000 GATGTGGTGAGCGGAGGATT 59.821 55.0 0.0 0.0 0.0 3.01 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
80 81 0.163788 CGCTCGAACGTGCAGAAAAT 59.836 50.000 18.32 0.00 34.68 1.82
163 164 2.194201 TCCTCCCATTGAACGGTTTC 57.806 50.000 0.00 0.00 0.00 2.78
199 200 2.496470 ACTACTGTTCCCTTCACGATCC 59.504 50.000 0.00 0.00 0.00 3.36
224 225 5.790593 TCCTAAGCTGACGTTTCTTGTTAT 58.209 37.500 0.00 0.00 0.00 1.89
251 252 4.926140 TGATATCTGATGAACGTCAGCT 57.074 40.909 16.38 11.09 44.15 4.24
288 289 4.545610 CAGCGAACTTTTCTTTATGGCAA 58.454 39.130 0.00 0.00 0.00 4.52
368 369 8.728088 AATTGTCATGTGTTTACGAAGAAATC 57.272 30.769 0.00 0.00 0.00 2.17
384 385 3.200825 AGAAATCGTCATCCTCCCACAAT 59.799 43.478 0.00 0.00 0.00 2.71
397 398 6.726379 TCCTCCCACAATGTAAATTGTCATA 58.274 36.000 8.38 0.00 42.32 2.15
425 426 3.270877 GTTCGTAATTGTCATGCCCTCT 58.729 45.455 0.00 0.00 0.00 3.69
426 427 3.179443 TCGTAATTGTCATGCCCTCTC 57.821 47.619 0.00 0.00 0.00 3.20
427 428 2.499693 TCGTAATTGTCATGCCCTCTCA 59.500 45.455 0.00 0.00 0.00 3.27
428 429 3.055458 TCGTAATTGTCATGCCCTCTCAA 60.055 43.478 0.00 0.00 0.00 3.02
429 430 3.063997 CGTAATTGTCATGCCCTCTCAAC 59.936 47.826 0.00 0.00 0.00 3.18
430 431 1.742761 ATTGTCATGCCCTCTCAACG 58.257 50.000 0.00 0.00 0.00 4.10
431 432 0.684535 TTGTCATGCCCTCTCAACGA 59.315 50.000 0.00 0.00 0.00 3.85
432 433 0.684535 TGTCATGCCCTCTCAACGAA 59.315 50.000 0.00 0.00 0.00 3.85
433 434 1.338105 TGTCATGCCCTCTCAACGAAG 60.338 52.381 0.00 0.00 0.00 3.79
434 435 1.066858 GTCATGCCCTCTCAACGAAGA 60.067 52.381 0.00 0.00 0.00 2.87
435 436 1.833630 TCATGCCCTCTCAACGAAGAT 59.166 47.619 0.00 0.00 0.00 2.40
436 437 1.938577 CATGCCCTCTCAACGAAGATG 59.061 52.381 0.00 0.00 0.00 2.90
437 438 0.391661 TGCCCTCTCAACGAAGATGC 60.392 55.000 0.00 0.00 0.00 3.91
439 440 1.649664 CCCTCTCAACGAAGATGCTG 58.350 55.000 0.00 0.00 0.00 4.41
564 572 4.033587 GGTGGCCGAAAAAGTTTCTTTTTC 59.966 41.667 25.16 25.16 42.10 2.29
728 740 4.699522 GCGCGAGTGGAAAGGGGT 62.700 66.667 12.10 0.00 0.00 4.95
847 862 3.904136 CCATTTCGATTCATGGCCTAC 57.096 47.619 3.32 0.00 33.75 3.18
888 907 1.336148 CCGCTATAAATACGTCGGCCA 60.336 52.381 2.24 0.00 0.00 5.36
936 955 3.324117 CACCATCATATTGCTCTCTCCG 58.676 50.000 0.00 0.00 0.00 4.63
937 956 2.289320 ACCATCATATTGCTCTCTCCGC 60.289 50.000 0.00 0.00 0.00 5.54
938 957 1.991264 CATCATATTGCTCTCTCCGCG 59.009 52.381 0.00 0.00 0.00 6.46
939 958 0.319040 TCATATTGCTCTCTCCGCGC 60.319 55.000 0.00 0.00 0.00 6.86
940 959 1.372251 ATATTGCTCTCTCCGCGCG 60.372 57.895 25.67 25.67 0.00 6.86
941 960 2.076622 ATATTGCTCTCTCCGCGCGT 62.077 55.000 29.95 8.36 0.00 6.01
946 965 1.939597 CTCTCTCCGCGCGTATACA 59.060 57.895 29.95 8.46 0.00 2.29
1166 1191 1.291132 GCCATCGTAAGCCTCTGTTC 58.709 55.000 0.00 0.00 37.18 3.18
1176 1201 1.991430 CCTCTGTTCGTTCGCATCG 59.009 57.895 0.00 0.00 0.00 3.84
1177 1202 1.341802 CTCTGTTCGTTCGCATCGC 59.658 57.895 0.00 0.00 0.00 4.58
1178 1203 1.344226 CTCTGTTCGTTCGCATCGCA 61.344 55.000 0.00 0.00 0.00 5.10
1179 1204 1.225475 CTGTTCGTTCGCATCGCAC 60.225 57.895 0.00 0.00 0.00 5.34
1180 1205 2.095843 GTTCGTTCGCATCGCACC 59.904 61.111 0.00 0.00 0.00 5.01
1228 1257 0.390603 TGCACCTGGTAATCGTTCCG 60.391 55.000 0.00 0.00 0.00 4.30
1263 1295 7.774157 TCTGGTCTTAGATATCACTTTACGACT 59.226 37.037 5.32 0.00 0.00 4.18
1346 1427 7.961325 TTTTATGGAATTGTTGCCTTCTTTC 57.039 32.000 0.00 0.00 0.00 2.62
1530 1612 2.074547 TTTTCATCGACACCGTCCTC 57.925 50.000 0.00 0.00 37.05 3.71
1699 1781 0.943673 CAACATGTGCAAGGTGACGA 59.056 50.000 0.00 0.00 0.00 4.20
1739 1823 5.345702 ACGCGTTGCTAGATTTCACTATAA 58.654 37.500 5.58 0.00 0.00 0.98
1741 1825 5.459107 CGCGTTGCTAGATTTCACTATAACT 59.541 40.000 0.00 0.00 0.00 2.24
1742 1826 6.019801 CGCGTTGCTAGATTTCACTATAACTT 60.020 38.462 0.00 0.00 0.00 2.66
1743 1827 7.464178 CGCGTTGCTAGATTTCACTATAACTTT 60.464 37.037 0.00 0.00 0.00 2.66
1744 1828 8.175716 GCGTTGCTAGATTTCACTATAACTTTT 58.824 33.333 0.00 0.00 0.00 2.27
1797 1898 2.440980 GGGCAAGGTGATGGAGGC 60.441 66.667 0.00 0.00 0.00 4.70
1816 1917 0.445436 CGATGCTGCAAGAACTGTCC 59.555 55.000 6.36 0.00 34.07 4.02
1870 1974 1.664321 GAGTGGTGTACCTCGGCGAT 61.664 60.000 11.27 0.00 36.82 4.58
2098 2202 2.351276 GGCGATCAGGTGGTGGTT 59.649 61.111 0.00 0.00 0.00 3.67
2243 2350 1.071228 TCGATGGAAGCATGGGAGATG 59.929 52.381 0.00 0.00 0.00 2.90
2312 6356 2.260481 GTTCCTTACGTCTACAGCAGC 58.740 52.381 0.00 0.00 0.00 5.25
2371 6417 3.160269 CTCTTGGAACTGGAAGCCAATT 58.840 45.455 0.00 0.00 40.59 2.32
2427 6637 4.467438 TGACATCCAGAAGCTGTTCTATCA 59.533 41.667 0.00 0.00 41.40 2.15
2442 7212 7.414540 GCTGTTCTATCACTAATTTGGGTCAAG 60.415 40.741 0.00 0.00 0.00 3.02
2546 7316 1.848886 ATCGGTCCCCACCCTTTCAC 61.849 60.000 0.00 0.00 40.01 3.18
2547 7317 2.526046 CGGTCCCCACCCTTTCACT 61.526 63.158 0.00 0.00 40.01 3.41
2554 7608 3.982052 TCCCCACCCTTTCACTTTAACTA 59.018 43.478 0.00 0.00 0.00 2.24
2569 7623 1.273759 AACTAACCGTTCCCTCCCTC 58.726 55.000 0.00 0.00 0.00 4.30
2575 7629 2.493501 GTTCCCTCCCTCGCGTAC 59.506 66.667 5.77 0.00 0.00 3.67
2591 7645 1.730851 GTACCCCCTTCCTCCCTATG 58.269 60.000 0.00 0.00 0.00 2.23
2606 7661 1.369625 CTATGTTTGGCTGGTCGACC 58.630 55.000 28.17 28.17 0.00 4.79
2615 7670 1.915614 GCTGGTCGACCGACTCGTTA 61.916 60.000 28.70 8.44 43.45 3.18
2628 7683 2.523015 ACTCGTTACCGCACTATTTCG 58.477 47.619 0.00 0.00 0.00 3.46
2633 7688 2.988493 GTTACCGCACTATTTCGTCACA 59.012 45.455 0.00 0.00 0.00 3.58
2647 7702 3.021695 TCGTCACAAGATACTACCCCAG 58.978 50.000 0.00 0.00 0.00 4.45
2669 7724 0.119155 ATGACCTCCCCAAGTCCAGA 59.881 55.000 0.00 0.00 31.76 3.86
2676 7731 0.909610 CCCCAAGTCCAGAGGTAGCA 60.910 60.000 0.00 0.00 0.00 3.49
2730 7785 4.023980 AGGACGAAAGGACACATGATAGA 58.976 43.478 0.00 0.00 0.00 1.98
2731 7786 4.651503 AGGACGAAAGGACACATGATAGAT 59.348 41.667 0.00 0.00 0.00 1.98
2752 7807 9.912461 ATAGATGGGTGGGGATAAAATAAAAAT 57.088 29.630 0.00 0.00 0.00 1.82
2754 7809 9.736819 AGATGGGTGGGGATAAAATAAAAATAA 57.263 29.630 0.00 0.00 0.00 1.40
2802 7857 6.702716 AATAGTAGTTCTTAGCGCTCTTCT 57.297 37.500 16.34 10.36 0.00 2.85
2803 7858 6.702716 ATAGTAGTTCTTAGCGCTCTTCTT 57.297 37.500 16.34 0.00 0.00 2.52
2804 7859 4.989044 AGTAGTTCTTAGCGCTCTTCTTC 58.011 43.478 16.34 4.95 0.00 2.87
2805 7860 3.944055 AGTTCTTAGCGCTCTTCTTCA 57.056 42.857 16.34 0.00 0.00 3.02
2806 7861 4.464069 AGTTCTTAGCGCTCTTCTTCAT 57.536 40.909 16.34 0.00 0.00 2.57
2807 7862 4.826556 AGTTCTTAGCGCTCTTCTTCATT 58.173 39.130 16.34 0.00 0.00 2.57
2808 7863 4.629200 AGTTCTTAGCGCTCTTCTTCATTG 59.371 41.667 16.34 0.00 0.00 2.82
2809 7864 4.193826 TCTTAGCGCTCTTCTTCATTGT 57.806 40.909 16.34 0.00 0.00 2.71
2810 7865 4.177026 TCTTAGCGCTCTTCTTCATTGTC 58.823 43.478 16.34 0.00 0.00 3.18
2811 7866 2.758736 AGCGCTCTTCTTCATTGTCT 57.241 45.000 2.64 0.00 0.00 3.41
2812 7867 3.051081 AGCGCTCTTCTTCATTGTCTT 57.949 42.857 2.64 0.00 0.00 3.01
2813 7868 3.406764 AGCGCTCTTCTTCATTGTCTTT 58.593 40.909 2.64 0.00 0.00 2.52
2814 7869 4.569943 AGCGCTCTTCTTCATTGTCTTTA 58.430 39.130 2.64 0.00 0.00 1.85
2815 7870 4.390297 AGCGCTCTTCTTCATTGTCTTTAC 59.610 41.667 2.64 0.00 0.00 2.01
2816 7871 4.436183 GCGCTCTTCTTCATTGTCTTTACC 60.436 45.833 0.00 0.00 0.00 2.85
2817 7872 4.932200 CGCTCTTCTTCATTGTCTTTACCT 59.068 41.667 0.00 0.00 0.00 3.08
2818 7873 5.409826 CGCTCTTCTTCATTGTCTTTACCTT 59.590 40.000 0.00 0.00 0.00 3.50
2819 7874 6.073003 CGCTCTTCTTCATTGTCTTTACCTTT 60.073 38.462 0.00 0.00 0.00 3.11
2820 7875 7.520614 CGCTCTTCTTCATTGTCTTTACCTTTT 60.521 37.037 0.00 0.00 0.00 2.27
2821 7876 8.138074 GCTCTTCTTCATTGTCTTTACCTTTTT 58.862 33.333 0.00 0.00 0.00 1.94
2822 7877 9.670719 CTCTTCTTCATTGTCTTTACCTTTTTC 57.329 33.333 0.00 0.00 0.00 2.29
2823 7878 9.408648 TCTTCTTCATTGTCTTTACCTTTTTCT 57.591 29.630 0.00 0.00 0.00 2.52
2832 7887 7.981142 TGTCTTTACCTTTTTCTATATTGCGG 58.019 34.615 0.00 0.00 0.00 5.69
2833 7888 7.066525 TGTCTTTACCTTTTTCTATATTGCGGG 59.933 37.037 0.00 0.00 0.00 6.13
2834 7889 7.281549 GTCTTTACCTTTTTCTATATTGCGGGA 59.718 37.037 0.00 0.00 0.00 5.14
2835 7890 7.996644 TCTTTACCTTTTTCTATATTGCGGGAT 59.003 33.333 0.00 0.00 0.00 3.85
2855 7910 5.871524 GGGATTTTCCTGCTTCATTTCTTTC 59.128 40.000 0.00 0.00 36.57 2.62
2861 7916 5.078949 TCCTGCTTCATTTCTTTCCATTCA 58.921 37.500 0.00 0.00 0.00 2.57
2865 7920 7.177832 TGCTTCATTTCTTTCCATTCATCAT 57.822 32.000 0.00 0.00 0.00 2.45
2866 7921 7.617225 TGCTTCATTTCTTTCCATTCATCATT 58.383 30.769 0.00 0.00 0.00 2.57
2954 8251 6.926630 TGATTATTTAAACTGGGGCAAAGT 57.073 33.333 0.00 0.00 0.00 2.66
3038 9150 5.596836 TGCAAGAACACCTTTGAAAATCT 57.403 34.783 0.00 0.00 31.42 2.40
3093 9205 5.886474 GGTATAAGAAGTTCCTTCCCTTTGG 59.114 44.000 0.00 0.00 40.98 3.28
3104 9216 7.834681 AGTTCCTTCCCTTTGGTAATTCTAATC 59.165 37.037 0.00 0.00 0.00 1.75
3107 9219 7.069344 CCTTCCCTTTGGTAATTCTAATCCAT 58.931 38.462 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.722700 TGAAGCGGGGCTCCTTGC 62.723 66.667 0.00 0.00 38.25 4.01
70 71 2.548057 TCCAACGTCAGATTTTCTGCAC 59.452 45.455 0.00 0.00 43.95 4.57
80 81 6.072728 CCAAATCTTACAAATCCAACGTCAGA 60.073 38.462 0.00 0.00 0.00 3.27
119 120 4.083862 AGCGCGAACCCCCTTCTC 62.084 66.667 12.10 0.00 0.00 2.87
127 128 4.162690 ATCCCCTCAGCGCGAACC 62.163 66.667 12.10 0.00 0.00 3.62
163 164 1.002087 AGTAGTTCCCCTGAGCAAACG 59.998 52.381 0.00 0.00 0.00 3.60
199 200 2.996621 CAAGAAACGTCAGCTTAGGAGG 59.003 50.000 0.00 0.00 0.00 4.30
240 241 2.289444 CCCTTTTCCTAGCTGACGTTCA 60.289 50.000 0.00 0.00 0.00 3.18
241 242 2.289506 ACCCTTTTCCTAGCTGACGTTC 60.290 50.000 0.00 0.00 0.00 3.95
245 246 2.615747 GGTCACCCTTTTCCTAGCTGAC 60.616 54.545 0.00 0.00 0.00 3.51
247 248 1.351017 TGGTCACCCTTTTCCTAGCTG 59.649 52.381 0.00 0.00 0.00 4.24
251 252 0.323629 CGCTGGTCACCCTTTTCCTA 59.676 55.000 0.00 0.00 0.00 2.94
288 289 2.167900 GCTATCTCCCACCACGTAAACT 59.832 50.000 0.00 0.00 0.00 2.66
329 330 9.288576 ACACATGACAATTTCTATGAAGAAGAA 57.711 29.630 0.00 0.00 42.60 2.52
368 369 2.979814 TACATTGTGGGAGGATGACG 57.020 50.000 0.00 0.00 0.00 4.35
397 398 6.978080 GGGCATGACAATTACGAACATTTTAT 59.022 34.615 0.00 0.00 0.00 1.40
414 415 1.066858 TCTTCGTTGAGAGGGCATGAC 60.067 52.381 0.00 0.00 0.00 3.06
419 420 0.107945 AGCATCTTCGTTGAGAGGGC 60.108 55.000 0.00 0.00 32.90 5.19
425 426 0.610174 AGAGGCAGCATCTTCGTTGA 59.390 50.000 3.00 0.00 0.00 3.18
426 427 1.005340 GAGAGGCAGCATCTTCGTTG 58.995 55.000 11.66 0.00 0.00 4.10
427 428 0.901124 AGAGAGGCAGCATCTTCGTT 59.099 50.000 11.66 0.00 0.00 3.85
428 429 0.459489 GAGAGAGGCAGCATCTTCGT 59.541 55.000 11.66 0.00 0.00 3.85
429 430 0.249405 GGAGAGAGGCAGCATCTTCG 60.249 60.000 11.66 0.00 0.00 3.79
430 431 0.829333 TGGAGAGAGGCAGCATCTTC 59.171 55.000 11.66 10.29 0.00 2.87
431 432 0.831966 CTGGAGAGAGGCAGCATCTT 59.168 55.000 11.66 1.20 0.00 2.40
432 433 1.688269 GCTGGAGAGAGGCAGCATCT 61.688 60.000 9.93 9.93 40.14 2.90
433 434 1.227615 GCTGGAGAGAGGCAGCATC 60.228 63.158 0.00 0.00 40.14 3.91
434 435 1.688269 GAGCTGGAGAGAGGCAGCAT 61.688 60.000 0.00 0.00 42.60 3.79
435 436 2.284478 AGCTGGAGAGAGGCAGCA 60.284 61.111 0.00 0.00 42.60 4.41
436 437 2.300850 CTGAGCTGGAGAGAGGCAGC 62.301 65.000 0.00 0.00 40.66 5.25
437 438 1.678598 CCTGAGCTGGAGAGAGGCAG 61.679 65.000 0.00 0.00 0.00 4.85
439 440 3.092780 GCCTGAGCTGGAGAGAGGC 62.093 68.421 0.00 0.00 42.37 4.70
564 572 1.370414 CGCCACCGTTGCTTTCAAG 60.370 57.895 0.00 0.00 31.93 3.02
728 740 1.378514 GCGGGATCTGGCTTTTCCA 60.379 57.895 0.00 0.00 44.18 3.53
847 862 2.125106 GCGACCTTGGTAGCCTGG 60.125 66.667 12.83 0.00 0.00 4.45
936 955 5.330295 AGCTAAGTATGTATGTATACGCGC 58.670 41.667 5.73 0.00 38.32 6.86
937 956 5.964168 GGAGCTAAGTATGTATGTATACGCG 59.036 44.000 3.53 3.53 38.32 6.01
938 957 7.066043 AGAGGAGCTAAGTATGTATGTATACGC 59.934 40.741 0.00 0.00 38.32 4.42
939 958 8.391859 CAGAGGAGCTAAGTATGTATGTATACG 58.608 40.741 0.00 0.00 38.32 3.06
940 959 9.233649 ACAGAGGAGCTAAGTATGTATGTATAC 57.766 37.037 0.00 0.00 34.48 1.47
941 960 9.809395 AACAGAGGAGCTAAGTATGTATGTATA 57.191 33.333 0.00 0.00 0.00 1.47
946 965 6.266558 CCAGAACAGAGGAGCTAAGTATGTAT 59.733 42.308 0.00 0.00 0.00 2.29
1166 1191 2.877113 TACGGTGCGATGCGAACG 60.877 61.111 0.00 0.00 36.05 3.95
1176 1201 1.296056 AAAGGCATCACGTACGGTGC 61.296 55.000 24.86 24.86 46.56 5.01
1178 1203 1.886886 AAAAAGGCATCACGTACGGT 58.113 45.000 21.06 2.13 0.00 4.83
1228 1257 7.545265 GTGATATCTAAGACCAGAGCAATCATC 59.455 40.741 3.98 0.00 30.89 2.92
1263 1295 4.511527 TGCTGAGATTTGGTTTGCAAAAA 58.488 34.783 14.67 5.27 0.00 1.94
1346 1427 2.358898 CCCATCATGGCGTCCTTTTAAG 59.641 50.000 0.00 0.00 35.79 1.85
1714 1798 2.157668 AGTGAAATCTAGCAACGCGTTG 59.842 45.455 40.07 40.07 43.14 4.10
1797 1898 0.445436 GGACAGTTCTTGCAGCATCG 59.555 55.000 0.00 0.00 0.00 3.84
1836 1940 1.153127 ACTCTACTCGGCCTCCTCG 60.153 63.158 0.00 0.00 0.00 4.63
1870 1974 2.056223 GCAGTAGTCGCCCCTACCA 61.056 63.158 4.30 0.00 38.46 3.25
2243 2350 4.769859 TTTACGTTGGGAAAGCCATTAC 57.230 40.909 0.00 0.00 35.15 1.89
2312 6356 3.057969 TCATGTCCCACACTTAAGCTG 57.942 47.619 1.29 3.10 0.00 4.24
2427 6637 9.533831 AAGTGATTAATCTTGACCCAAATTAGT 57.466 29.630 16.24 0.00 0.00 2.24
2442 7212 6.828785 TCCCTAAAAGAGGCAAGTGATTAATC 59.171 38.462 8.60 8.60 45.17 1.75
2513 7283 4.320870 GGGACCGATGACAAGAAAAACTA 58.679 43.478 0.00 0.00 0.00 2.24
2546 7316 3.262660 AGGGAGGGAACGGTTAGTTAAAG 59.737 47.826 0.00 0.00 44.35 1.85
2547 7317 3.250617 AGGGAGGGAACGGTTAGTTAAA 58.749 45.455 0.00 0.00 44.35 1.52
2554 7608 3.703127 GCGAGGGAGGGAACGGTT 61.703 66.667 0.00 0.00 0.00 4.44
2569 7623 3.846430 GGAGGAAGGGGGTACGCG 61.846 72.222 3.53 3.53 44.67 6.01
2575 7629 1.215423 CAAACATAGGGAGGAAGGGGG 59.785 57.143 0.00 0.00 0.00 5.40
2591 7645 2.029964 TCGGTCGACCAGCCAAAC 59.970 61.111 32.80 4.76 35.14 2.93
2615 7670 2.066262 CTTGTGACGAAATAGTGCGGT 58.934 47.619 0.00 0.00 0.00 5.68
2628 7683 2.500098 TGCTGGGGTAGTATCTTGTGAC 59.500 50.000 0.00 0.00 0.00 3.67
2633 7688 3.136626 GGTCATTGCTGGGGTAGTATCTT 59.863 47.826 0.00 0.00 0.00 2.40
2647 7702 0.681243 GGACTTGGGGAGGTCATTGC 60.681 60.000 0.00 0.00 34.49 3.56
2669 7724 0.687757 TGAGCGGAGGATTGCTACCT 60.688 55.000 0.00 0.00 42.60 3.08
2676 7731 0.179000 GATGTGGTGAGCGGAGGATT 59.821 55.000 0.00 0.00 0.00 3.01
2713 7768 4.818546 CACCCATCTATCATGTGTCCTTTC 59.181 45.833 0.00 0.00 0.00 2.62
2722 7777 5.519183 TTTATCCCCACCCATCTATCATG 57.481 43.478 0.00 0.00 0.00 3.07
2781 7836 5.646793 TGAAGAAGAGCGCTAAGAACTACTA 59.353 40.000 11.50 0.00 0.00 1.82
2783 7838 4.734917 TGAAGAAGAGCGCTAAGAACTAC 58.265 43.478 11.50 0.00 0.00 2.73
2806 7861 8.455682 CCGCAATATAGAAAAAGGTAAAGACAA 58.544 33.333 0.00 0.00 0.00 3.18
2807 7862 7.066525 CCCGCAATATAGAAAAAGGTAAAGACA 59.933 37.037 0.00 0.00 0.00 3.41
2808 7863 7.281549 TCCCGCAATATAGAAAAAGGTAAAGAC 59.718 37.037 0.00 0.00 0.00 3.01
2809 7864 7.340256 TCCCGCAATATAGAAAAAGGTAAAGA 58.660 34.615 0.00 0.00 0.00 2.52
2810 7865 7.562454 TCCCGCAATATAGAAAAAGGTAAAG 57.438 36.000 0.00 0.00 0.00 1.85
2811 7866 8.528044 AATCCCGCAATATAGAAAAAGGTAAA 57.472 30.769 0.00 0.00 0.00 2.01
2812 7867 8.528044 AAATCCCGCAATATAGAAAAAGGTAA 57.472 30.769 0.00 0.00 0.00 2.85
2813 7868 8.528044 AAAATCCCGCAATATAGAAAAAGGTA 57.472 30.769 0.00 0.00 0.00 3.08
2814 7869 7.417456 GGAAAATCCCGCAATATAGAAAAAGGT 60.417 37.037 0.00 0.00 0.00 3.50
2815 7870 6.923508 GGAAAATCCCGCAATATAGAAAAAGG 59.076 38.462 0.00 0.00 0.00 3.11
2816 7871 7.649306 CAGGAAAATCCCGCAATATAGAAAAAG 59.351 37.037 0.00 0.00 37.19 2.27
2817 7872 7.488322 CAGGAAAATCCCGCAATATAGAAAAA 58.512 34.615 0.00 0.00 37.19 1.94
2818 7873 6.460953 GCAGGAAAATCCCGCAATATAGAAAA 60.461 38.462 0.00 0.00 37.19 2.29
2819 7874 5.009610 GCAGGAAAATCCCGCAATATAGAAA 59.990 40.000 0.00 0.00 37.19 2.52
2820 7875 4.518970 GCAGGAAAATCCCGCAATATAGAA 59.481 41.667 0.00 0.00 37.19 2.10
2821 7876 4.072131 GCAGGAAAATCCCGCAATATAGA 58.928 43.478 0.00 0.00 37.19 1.98
2822 7877 4.074970 AGCAGGAAAATCCCGCAATATAG 58.925 43.478 7.31 0.00 37.19 1.31
2823 7878 4.098914 AGCAGGAAAATCCCGCAATATA 57.901 40.909 7.31 0.00 37.19 0.86
2824 7879 2.949447 AGCAGGAAAATCCCGCAATAT 58.051 42.857 7.31 0.00 37.19 1.28
2825 7880 2.435372 AGCAGGAAAATCCCGCAATA 57.565 45.000 7.31 0.00 37.19 1.90
2826 7881 1.478105 GAAGCAGGAAAATCCCGCAAT 59.522 47.619 7.31 0.00 37.19 3.56
2827 7882 0.887933 GAAGCAGGAAAATCCCGCAA 59.112 50.000 7.31 0.00 37.19 4.85
2828 7883 0.251121 TGAAGCAGGAAAATCCCGCA 60.251 50.000 7.31 0.00 37.19 5.69
2829 7884 1.106285 ATGAAGCAGGAAAATCCCGC 58.894 50.000 0.00 0.00 37.19 6.13
2830 7885 3.445096 AGAAATGAAGCAGGAAAATCCCG 59.555 43.478 0.00 0.00 37.19 5.14
2831 7886 5.411831 AAGAAATGAAGCAGGAAAATCCC 57.588 39.130 0.00 0.00 37.19 3.85
2832 7887 5.871524 GGAAAGAAATGAAGCAGGAAAATCC 59.128 40.000 0.00 0.00 36.58 3.01
2833 7888 6.458210 TGGAAAGAAATGAAGCAGGAAAATC 58.542 36.000 0.00 0.00 0.00 2.17
2834 7889 6.423776 TGGAAAGAAATGAAGCAGGAAAAT 57.576 33.333 0.00 0.00 0.00 1.82
2835 7890 5.867903 TGGAAAGAAATGAAGCAGGAAAA 57.132 34.783 0.00 0.00 0.00 2.29
3038 9150 4.780815 ACAGGTCAGAAAGTGATTTGTCA 58.219 39.130 0.00 0.00 37.56 3.58


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

AutoCloner maintained by Alex Coulton.