Multiple sequence alignment - TraesCS2B01G496600

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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 TraesCS2B01G496600 chr2B 100.000 3948 0 0 1 3948 693317195 693313248 0.000000e+00 7291.0
1 TraesCS2B01G496600 chr2B 85.042 361 30 11 2590 2947 693308000 693307661 2.920000e-91 346.0
2 TraesCS2B01G496600 chr2B 89.157 83 9 0 2932 3014 693306061 693305979 1.940000e-18 104.0
3 TraesCS2B01G496600 chr2D 91.435 2265 148 25 812 3047 577078656 577076409 0.000000e+00 3066.0
4 TraesCS2B01G496600 chr2D 91.176 204 17 1 2811 3014 577024061 577023859 3.890000e-70 276.0
5 TraesCS2B01G496600 chr2A 89.685 2288 129 44 812 3047 715251343 715249111 0.000000e+00 2819.0
6 TraesCS2B01G496600 chr2A 86.623 912 84 25 3044 3948 715220987 715220107 0.000000e+00 974.0
7 TraesCS2B01G496600 chr2A 85.662 823 68 20 1 804 715268185 715267394 0.000000e+00 821.0
8 TraesCS2B01G496600 chr7D 87.267 589 54 14 20 598 82450727 82450150 0.000000e+00 652.0
9 TraesCS2B01G496600 chr7A 85.811 592 66 13 20 601 84249765 84249182 2.610000e-171 612.0
10 TraesCS2B01G496600 chr7B 83.559 590 68 21 20 597 30770917 30770345 3.490000e-145 525.0
11 TraesCS2B01G496600 chr7B 82.776 598 69 18 20 598 31449696 31449114 1.640000e-138 503.0
12 TraesCS2B01G496600 chr3B 86.275 51 5 2 3323 3373 410615746 410615698 2.000000e-03 54.7
13 TraesCS2B01G496600 chr3A 86.275 51 5 2 3323 3373 421716953 421716905 2.000000e-03 54.7


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 TraesCS2B01G496600 chr2B 693313248 693317195 3947 True 7291 7291 100.0000 1 3948 1 chr2B.!!$R1 3947
1 TraesCS2B01G496600 chr2B 693305979 693308000 2021 True 225 346 87.0995 2590 3014 2 chr2B.!!$R2 424
2 TraesCS2B01G496600 chr2D 577076409 577078656 2247 True 3066 3066 91.4350 812 3047 1 chr2D.!!$R2 2235
3 TraesCS2B01G496600 chr2A 715249111 715251343 2232 True 2819 2819 89.6850 812 3047 1 chr2A.!!$R2 2235
4 TraesCS2B01G496600 chr2A 715220107 715220987 880 True 974 974 86.6230 3044 3948 1 chr2A.!!$R1 904
5 TraesCS2B01G496600 chr2A 715267394 715268185 791 True 821 821 85.6620 1 804 1 chr2A.!!$R3 803
6 TraesCS2B01G496600 chr7D 82450150 82450727 577 True 652 652 87.2670 20 598 1 chr7D.!!$R1 578
7 TraesCS2B01G496600 chr7A 84249182 84249765 583 True 612 612 85.8110 20 601 1 chr7A.!!$R1 581
8 TraesCS2B01G496600 chr7B 30770345 30770917 572 True 525 525 83.5590 20 597 1 chr7B.!!$R1 577
9 TraesCS2B01G496600 chr7B 31449114 31449696 582 True 503 503 82.7760 20 598 1 chr7B.!!$R2 578

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
43 44 0.323629 AAATCCTTCCGTTCAGCCGA 59.676 50.0 0.00 0.0 0.00 5.54 F
342 353 0.391966 TCTAGGCGCGTCTCTAGCTA 59.608 55.0 20.54 0.0 34.52 3.32 F
1026 1066 0.530744 GGAAAAGGAAATCCACCGCC 59.469 55.0 1.67 0.0 38.89 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1359 1441 0.530744 CACGCCTGCCTGTAACTCTA 59.469 55.0 0.00 0.0 0.00 2.43 R
1747 1839 0.601558 GTCGCAGGTCTCAACTGGTA 59.398 55.0 0.00 0.0 36.48 3.25 R
2961 4674 0.320683 CACCGATCAGTGGAACAGCA 60.321 55.0 0.76 0.0 41.80 4.41 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
43 44 0.323629 AAATCCTTCCGTTCAGCCGA 59.676 50.000 0.00 0.00 0.00 5.54
80 81 2.031857 GCGTCGACCTTCTCTATCGAAT 60.032 50.000 10.58 0.00 45.65 3.34
87 88 3.046390 CCTTCTCTATCGAATGACACGC 58.954 50.000 0.00 0.00 0.00 5.34
98 99 0.534203 ATGACACGCGTCCCTGTTTT 60.534 50.000 9.86 0.00 41.85 2.43
182 183 2.025510 CCTCTCCCAGGCATTCTTCTTT 60.026 50.000 0.00 0.00 34.56 2.52
192 193 5.707298 CAGGCATTCTTCTTTCCTTCTGTTA 59.293 40.000 0.00 0.00 0.00 2.41
342 353 0.391966 TCTAGGCGCGTCTCTAGCTA 59.608 55.000 20.54 0.00 34.52 3.32
385 396 1.029408 GGTGTTGTGAGTGTGTGCCA 61.029 55.000 0.00 0.00 0.00 4.92
423 434 5.394553 GGACAAATTTCCATAGCTTTCCTGG 60.395 44.000 0.00 0.00 35.49 4.45
535 546 4.060038 TCTGAACAAGACCTCAGTTGAC 57.940 45.455 0.00 0.00 40.06 3.18
569 587 6.037391 CACAACAAGATCTTGGTTGCAAATTT 59.963 34.615 33.11 16.00 44.45 1.82
570 588 7.224362 CACAACAAGATCTTGGTTGCAAATTTA 59.776 33.333 33.11 0.00 44.45 1.40
571 589 7.933033 ACAACAAGATCTTGGTTGCAAATTTAT 59.067 29.630 33.11 15.81 44.45 1.40
632 650 9.874205 AAAAATTCATAATATGACCTGTGTTGG 57.126 29.630 1.88 0.00 39.39 3.77
634 652 9.425248 AAATTCATAATATGACCTGTGTTGGAT 57.575 29.630 1.88 0.00 39.39 3.41
669 705 1.202114 GATCCGATGTTTTGCAAGGCA 59.798 47.619 0.00 3.23 36.47 4.75
670 706 0.597568 TCCGATGTTTTGCAAGGCAG 59.402 50.000 0.00 0.00 40.61 4.85
674 710 2.356194 GTTTTGCAAGGCAGCGGG 60.356 61.111 0.00 0.00 40.61 6.13
690 726 4.385748 GCAGCGGGTCTTTTAAAAAGATTG 59.614 41.667 1.66 0.00 0.00 2.67
693 729 4.242475 CGGGTCTTTTAAAAAGATTGGCC 58.758 43.478 0.00 0.00 0.00 5.36
698 734 0.899019 TTAAAAAGATTGGCCGGCCC 59.101 50.000 41.75 26.88 34.56 5.80
709 745 3.795342 CCGGCCCACGCGTAAAAG 61.795 66.667 13.44 0.00 42.52 2.27
719 755 1.302383 CGCGTAAAAGTGCCCATGGA 61.302 55.000 15.22 0.00 0.00 3.41
728 764 3.498774 AGTGCCCATGGATAAAGCTAG 57.501 47.619 15.22 0.00 0.00 3.42
730 766 1.425066 TGCCCATGGATAAAGCTAGGG 59.575 52.381 15.22 0.00 37.87 3.53
737 773 5.163195 CCATGGATAAAGCTAGGGTACACTT 60.163 44.000 5.56 0.00 0.00 3.16
766 802 2.217112 CGAAGCTATGCTACACGCC 58.783 57.895 0.00 0.00 38.25 5.68
778 814 0.540133 TACACGCCTACACCTGGACA 60.540 55.000 0.00 0.00 0.00 4.02
848 884 3.086282 TCACTTGGCTCGATACACACTA 58.914 45.455 0.00 0.00 0.00 2.74
1008 1048 4.936575 CATCATGGGATGGTGGGG 57.063 61.111 0.00 0.00 45.84 4.96
1026 1066 0.530744 GGAAAAGGAAATCCACCGCC 59.469 55.000 1.67 0.00 38.89 6.13
1201 1275 1.470112 GCGAGCTCCTCCAGTTAGTTC 60.470 57.143 8.47 0.00 0.00 3.01
1210 1284 3.254892 CTCCAGTTAGTTCCTTCGCTTC 58.745 50.000 0.00 0.00 0.00 3.86
1213 1287 3.433615 CCAGTTAGTTCCTTCGCTTCAAG 59.566 47.826 0.00 0.00 0.00 3.02
1216 1290 2.622064 AGTTCCTTCGCTTCAAGTGT 57.378 45.000 0.00 0.00 0.00 3.55
1222 1296 2.160417 CCTTCGCTTCAAGTGTTGGATC 59.840 50.000 0.00 0.00 0.00 3.36
1223 1297 1.428448 TCGCTTCAAGTGTTGGATCG 58.572 50.000 0.00 0.00 0.00 3.69
1274 1354 2.476051 CGGTCGCTGCAATGTGTC 59.524 61.111 0.00 0.00 0.00 3.67
1278 1358 1.672030 TCGCTGCAATGTGTCCTGG 60.672 57.895 0.00 0.00 0.00 4.45
1279 1359 2.570181 GCTGCAATGTGTCCTGGC 59.430 61.111 0.00 0.00 0.00 4.85
1330 1412 8.424133 TGCATTCTGTTCTGTACATGATACTAT 58.576 33.333 0.00 0.00 35.85 2.12
1401 1487 3.181465 GGATTGGTCTCGGATTTCTGCTA 60.181 47.826 0.00 0.00 0.00 3.49
1413 1499 5.048504 CGGATTTCTGCTACTAACCCGTATA 60.049 44.000 0.00 0.00 0.00 1.47
1421 1507 8.042515 TCTGCTACTAACCCGTATATTTTGTTT 58.957 33.333 0.00 0.00 0.00 2.83
1627 1714 7.884877 ACTAAATTGTCATCAGATCCAGTTCAA 59.115 33.333 0.00 0.00 0.00 2.69
1629 1716 5.947228 TTGTCATCAGATCCAGTTCAAAC 57.053 39.130 0.00 0.00 0.00 2.93
1639 1726 6.206243 CAGATCCAGTTCAAACAGTTCTGAAT 59.794 38.462 6.83 0.00 35.50 2.57
1642 1729 6.064060 TCCAGTTCAAACAGTTCTGAATGAT 58.936 36.000 6.83 3.07 34.26 2.45
1681 1769 0.869730 CTTTGCCATTGCCAAACTGC 59.130 50.000 0.00 0.00 36.33 4.40
1688 1776 2.506444 CATTGCCAAACTGCCCATTTT 58.494 42.857 0.00 0.00 0.00 1.82
1694 1782 3.066380 CCAAACTGCCCATTTTAGCAAC 58.934 45.455 0.00 0.00 38.82 4.17
1698 1786 3.993920 ACTGCCCATTTTAGCAACAAAG 58.006 40.909 0.00 0.00 38.82 2.77
1716 1808 7.254898 GCAACAAAGCTGCTATTCATATACAGA 60.255 37.037 0.90 0.00 36.84 3.41
1717 1809 8.615211 CAACAAAGCTGCTATTCATATACAGAA 58.385 33.333 0.90 0.00 0.00 3.02
1742 1834 7.939784 AAAAAGAAACAGAGACAGTAAGGTT 57.060 32.000 0.00 0.00 0.00 3.50
1744 1836 8.434733 AAAAGAAACAGAGACAGTAAGGTTAC 57.565 34.615 0.00 0.00 0.00 2.50
1745 1837 6.099159 AGAAACAGAGACAGTAAGGTTACC 57.901 41.667 0.00 0.00 34.19 2.85
1747 1839 6.326843 AGAAACAGAGACAGTAAGGTTACCTT 59.673 38.462 21.14 21.14 46.63 3.50
1761 1855 3.581770 GGTTACCTTACCAGTTGAGACCT 59.418 47.826 0.00 0.00 38.12 3.85
1892 1986 1.641577 GTCCCTCTCAAATTCGACGG 58.358 55.000 0.00 0.00 0.00 4.79
1953 2047 1.090052 CCGCCAAGAACTTCGATCCC 61.090 60.000 0.00 0.00 0.00 3.85
1983 2077 2.047179 GGCAGGTGGTTCGAGGTC 60.047 66.667 0.00 0.00 0.00 3.85
1991 2085 2.202623 GTTCGAGGTCGCATCGCT 60.203 61.111 8.62 0.00 39.98 4.93
1996 2090 1.710339 GAGGTCGCATCGCTCAAAC 59.290 57.895 0.00 0.00 0.00 2.93
2081 2175 6.018098 CAGCCTCATACTGAACAATCTGAATC 60.018 42.308 0.00 0.00 37.32 2.52
2111 2205 6.998074 TGTTGTTGTTGAGGAAGACAGAATAT 59.002 34.615 0.00 0.00 0.00 1.28
2147 2244 8.030692 TGTCTGAAAAATAAATTGGCATCTCAG 58.969 33.333 0.00 0.00 0.00 3.35
2152 2249 9.173939 GAAAAATAAATTGGCATCTCAGTATCG 57.826 33.333 0.00 0.00 0.00 2.92
2154 2251 7.426929 AATAAATTGGCATCTCAGTATCGAC 57.573 36.000 0.00 0.00 0.00 4.20
2165 2262 7.597386 CATCTCAGTATCGACCTGAATTATCA 58.403 38.462 15.27 0.45 38.42 2.15
2228 2325 3.134458 GCTGCAGGGAGTGTATACATTC 58.866 50.000 17.12 17.62 32.58 2.67
2414 2511 3.691342 CGCTTCCCGACACTCCCA 61.691 66.667 0.00 0.00 40.02 4.37
2444 2541 3.244353 CCAAGCTACCCTATGATGTCCTG 60.244 52.174 0.00 0.00 0.00 3.86
2456 2553 1.683917 GATGTCCTGGCGACTGACTAT 59.316 52.381 11.87 5.10 42.49 2.12
2561 2658 7.192852 ACTCATGTCTAACCATCTTGAGAAT 57.807 36.000 12.01 0.00 37.06 2.40
2605 2702 7.540299 AGATTCTAGAGTGTAGTACTTTGTGC 58.460 38.462 0.00 0.00 40.53 4.57
2613 2710 5.878116 AGTGTAGTACTTTGTGCTGTTGAAA 59.122 36.000 0.00 0.00 35.67 2.69
2623 2720 3.249799 TGTGCTGTTGAAATCACCTAACG 59.750 43.478 0.00 0.00 0.00 3.18
2624 2721 3.250040 GTGCTGTTGAAATCACCTAACGT 59.750 43.478 0.00 0.00 0.00 3.99
2636 2733 3.067106 CACCTAACGTTCTGATGCACTT 58.933 45.455 2.82 0.00 0.00 3.16
2653 2751 8.186163 TGATGCACTTGTGATCTGAAAATAATC 58.814 33.333 4.79 0.00 0.00 1.75
2660 2759 7.312657 TGTGATCTGAAAATAATCTGTCTGC 57.687 36.000 0.00 0.00 0.00 4.26
2695 2794 1.675552 ACTCAAGAACACCAAACCCG 58.324 50.000 0.00 0.00 0.00 5.28
2701 2800 2.627839 GAACACCAAACCCGGGACCA 62.628 60.000 32.02 0.00 0.00 4.02
2725 2825 4.724303 AGTTCATCGAGAAGTACAAGTCG 58.276 43.478 0.00 0.00 38.12 4.18
2734 2834 1.154150 GTACAAGTCGTACGCCGCT 60.154 57.895 11.24 5.71 41.13 5.52
2827 2927 2.203394 ATGATGTCCATGCCCGGC 60.203 61.111 1.04 1.04 33.39 6.13
2961 4674 6.783708 TTTCAAGTAAACACAAACCCATCT 57.216 33.333 0.00 0.00 0.00 2.90
3016 4729 2.666619 CGGAAGCTGCACTTTTGATGAC 60.667 50.000 1.02 0.00 39.29 3.06
3021 4734 4.553323 AGCTGCACTTTTGATGACAAATC 58.447 39.130 1.02 0.00 43.99 2.17
3053 4766 4.228210 TCCCTTCAGTGGCTTCATCTAATT 59.772 41.667 0.00 0.00 0.00 1.40
3085 4798 1.656587 ATTGGAGGACCTAGTGCACA 58.343 50.000 21.04 4.13 37.04 4.57
3092 4805 3.374764 AGGACCTAGTGCACATGATACA 58.625 45.455 21.04 0.00 0.00 2.29
3099 4812 6.051074 CCTAGTGCACATGATACATTCTCAA 58.949 40.000 21.04 0.00 0.00 3.02
3105 4818 7.219535 GTGCACATGATACATTCTCAAAACATC 59.780 37.037 13.17 0.00 0.00 3.06
3110 4823 7.761651 TGATACATTCTCAAAACATCTCTCG 57.238 36.000 0.00 0.00 0.00 4.04
3117 4830 7.397892 TTCTCAAAACATCTCTCGTCTCTAT 57.602 36.000 0.00 0.00 0.00 1.98
3133 4846 5.294552 CGTCTCTATTCCATCCCAAAGAAAC 59.705 44.000 0.00 0.00 0.00 2.78
3134 4847 5.294552 GTCTCTATTCCATCCCAAAGAAACG 59.705 44.000 0.00 0.00 0.00 3.60
3140 4853 1.265635 CATCCCAAAGAAACGCACGAA 59.734 47.619 0.00 0.00 0.00 3.85
3145 4858 4.036498 TCCCAAAGAAACGCACGAATTTTA 59.964 37.500 0.00 0.00 0.00 1.52
3150 4863 7.848539 CCAAAGAAACGCACGAATTTTATTTTT 59.151 29.630 0.00 0.00 0.00 1.94
3151 4864 8.660315 CAAAGAAACGCACGAATTTTATTTTTG 58.340 29.630 0.00 0.00 0.00 2.44
3152 4865 7.458038 AGAAACGCACGAATTTTATTTTTGT 57.542 28.000 0.00 0.00 0.00 2.83
3153 4866 7.901002 AGAAACGCACGAATTTTATTTTTGTT 58.099 26.923 0.00 0.00 0.00 2.83
3154 4867 8.384365 AGAAACGCACGAATTTTATTTTTGTTT 58.616 25.926 0.00 0.00 0.00 2.83
3155 4868 9.621046 GAAACGCACGAATTTTATTTTTGTTTA 57.379 25.926 0.00 0.00 0.00 2.01
3156 4869 8.959761 AACGCACGAATTTTATTTTTGTTTAC 57.040 26.923 0.00 0.00 0.00 2.01
3157 4870 8.116624 ACGCACGAATTTTATTTTTGTTTACA 57.883 26.923 0.00 0.00 0.00 2.41
3158 4871 8.592998 ACGCACGAATTTTATTTTTGTTTACAA 58.407 25.926 0.00 0.00 0.00 2.41
3159 4872 9.409949 CGCACGAATTTTATTTTTGTTTACAAA 57.590 25.926 4.02 4.02 43.36 2.83
3187 4900 8.994429 ATGTTCAGTATCTCTCACACTAAAAG 57.006 34.615 0.00 0.00 0.00 2.27
3236 4949 5.139727 TCAAATTCCTTGTCACATGACCTT 58.860 37.500 9.48 0.00 44.15 3.50
3242 4955 5.305585 TCCTTGTCACATGACCTTTAGAAC 58.694 41.667 9.48 0.00 44.15 3.01
3252 4965 9.166173 CACATGACCTTTAGAACAAGATCAATA 57.834 33.333 0.00 0.00 29.61 1.90
3361 5074 5.181245 AGTCTTGGGATACATTTCAAACACG 59.819 40.000 0.00 0.00 39.74 4.49
3369 5082 9.198837 GGGATACATTTCAAACACGTTTAAATT 57.801 29.630 0.00 0.00 39.74 1.82
3408 5121 8.912988 TCATTTATTTCACTCAACCTTTTCAGT 58.087 29.630 0.00 0.00 0.00 3.41
3443 5156 6.303839 TCTTATTTGTCAAGCTGGGTACTTT 58.696 36.000 0.00 0.00 0.00 2.66
3447 5160 4.699925 TGTCAAGCTGGGTACTTTAGTT 57.300 40.909 0.00 0.00 0.00 2.24
3557 5272 9.977762 GCTTATTTCATTCATTTCAATTTCACC 57.022 29.630 0.00 0.00 0.00 4.02
3580 5295 9.208022 CACCTATATTTCACATATACCAGTGTG 57.792 37.037 0.00 0.00 45.37 3.82
3587 5302 6.978343 TCACATATACCAGTGTGCTTAAAC 57.022 37.500 0.87 0.00 44.05 2.01
3590 5305 7.445707 TCACATATACCAGTGTGCTTAAACAAA 59.554 33.333 0.87 0.00 44.05 2.83
3591 5306 8.079203 CACATATACCAGTGTGCTTAAACAAAA 58.921 33.333 0.00 0.00 39.23 2.44
3592 5307 8.802267 ACATATACCAGTGTGCTTAAACAAAAT 58.198 29.630 0.00 0.00 0.00 1.82
3708 5423 9.650714 AGGATTGAAATCAGGATTTTATGATGA 57.349 29.630 8.53 0.00 40.77 2.92
3802 5517 9.874205 TTTGAAATGAGTGAGTTTTTGAAATCT 57.126 25.926 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.426667 AGGATTTCCCTTACCCAAATGATAAA 58.573 34.615 0.00 0.00 44.85 1.40
34 35 1.392510 GTTGTAATCCGTCGGCTGAAC 59.607 52.381 6.34 2.78 0.00 3.18
43 44 3.334078 CGCCTACGTTGTAATCCGT 57.666 52.632 0.00 0.00 40.87 4.69
56 57 2.492012 GATAGAGAAGGTCGACGCCTA 58.508 52.381 9.92 6.49 38.03 3.93
69 70 2.286242 GACGCGTGTCATTCGATAGAGA 60.286 50.000 20.70 0.00 45.79 3.10
182 183 5.313712 GGTGGTGAGAAATTAACAGAAGGA 58.686 41.667 0.00 0.00 0.00 3.36
192 193 1.219213 TGGTTGGGGTGGTGAGAAATT 59.781 47.619 0.00 0.00 0.00 1.82
325 336 1.440708 GATAGCTAGAGACGCGCCTA 58.559 55.000 5.73 4.57 0.00 3.93
360 371 2.287769 CACACTCACAACACCATGTCA 58.712 47.619 0.00 0.00 0.00 3.58
395 406 1.067060 GCTATGGAAATTTGTCCCCGC 59.933 52.381 0.00 0.00 36.80 6.13
396 407 2.654863 AGCTATGGAAATTTGTCCCCG 58.345 47.619 0.00 0.00 36.80 5.73
513 524 4.101585 TGTCAACTGAGGTCTTGTTCAGAT 59.898 41.667 8.35 0.00 42.67 2.90
517 528 5.560966 TTTTGTCAACTGAGGTCTTGTTC 57.439 39.130 0.00 0.00 0.00 3.18
544 562 3.713858 TGCAACCAAGATCTTGTTGTG 57.286 42.857 30.07 25.06 38.85 3.33
545 563 4.734398 TTTGCAACCAAGATCTTGTTGT 57.266 36.364 30.07 22.44 38.85 3.32
608 626 8.821686 TCCAACACAGGTCATATTATGAATTT 57.178 30.769 7.93 0.00 41.69 1.82
611 629 7.805163 AGATCCAACACAGGTCATATTATGAA 58.195 34.615 7.93 0.00 41.69 2.57
612 630 7.379059 AGATCCAACACAGGTCATATTATGA 57.621 36.000 2.14 2.14 36.84 2.15
615 633 7.552687 GTCAAAGATCCAACACAGGTCATATTA 59.447 37.037 0.00 0.00 0.00 0.98
618 636 5.013079 AGTCAAAGATCCAACACAGGTCATA 59.987 40.000 0.00 0.00 0.00 2.15
620 638 3.136443 AGTCAAAGATCCAACACAGGTCA 59.864 43.478 0.00 0.00 0.00 4.02
622 640 3.496870 GGAGTCAAAGATCCAACACAGGT 60.497 47.826 0.00 0.00 35.54 4.00
625 643 2.766313 CGGAGTCAAAGATCCAACACA 58.234 47.619 0.00 0.00 35.14 3.72
626 644 1.464997 GCGGAGTCAAAGATCCAACAC 59.535 52.381 0.00 0.00 35.14 3.32
632 650 2.478831 GATCAGGCGGAGTCAAAGATC 58.521 52.381 0.00 0.00 32.27 2.75
634 652 0.537188 GGATCAGGCGGAGTCAAAGA 59.463 55.000 0.00 0.00 0.00 2.52
669 705 4.560716 GCCAATCTTTTTAAAAGACCCGCT 60.561 41.667 20.54 3.76 0.00 5.52
670 706 3.678072 GCCAATCTTTTTAAAAGACCCGC 59.322 43.478 20.54 16.93 0.00 6.13
674 710 3.678072 GCCGGCCAATCTTTTTAAAAGAC 59.322 43.478 20.54 9.23 0.00 3.01
693 729 3.045492 ACTTTTACGCGTGGGCCG 61.045 61.111 24.59 8.88 40.40 6.13
698 734 0.454285 CATGGGCACTTTTACGCGTG 60.454 55.000 24.59 7.50 0.00 5.34
704 740 4.609301 AGCTTTATCCATGGGCACTTTTA 58.391 39.130 13.02 0.00 0.00 1.52
706 742 3.105959 AGCTTTATCCATGGGCACTTT 57.894 42.857 13.02 0.00 0.00 2.66
709 745 2.508526 CCTAGCTTTATCCATGGGCAC 58.491 52.381 13.02 0.00 0.00 5.01
758 794 0.172803 GTCCAGGTGTAGGCGTGTAG 59.827 60.000 0.00 0.00 0.00 2.74
759 795 0.540133 TGTCCAGGTGTAGGCGTGTA 60.540 55.000 0.00 0.00 0.00 2.90
760 796 1.192146 ATGTCCAGGTGTAGGCGTGT 61.192 55.000 0.00 0.00 0.00 4.49
761 797 0.821517 TATGTCCAGGTGTAGGCGTG 59.178 55.000 0.00 0.00 0.00 5.34
762 798 0.822164 GTATGTCCAGGTGTAGGCGT 59.178 55.000 0.00 0.00 0.00 5.68
763 799 1.112113 AGTATGTCCAGGTGTAGGCG 58.888 55.000 0.00 0.00 0.00 5.52
764 800 4.344102 TCAATAGTATGTCCAGGTGTAGGC 59.656 45.833 0.00 0.00 0.00 3.93
765 801 6.479972 TTCAATAGTATGTCCAGGTGTAGG 57.520 41.667 0.00 0.00 0.00 3.18
766 802 8.786826 TTTTTCAATAGTATGTCCAGGTGTAG 57.213 34.615 0.00 0.00 0.00 2.74
807 843 1.202675 AGTGGCCCGTCGAGTTAAAAA 60.203 47.619 0.00 0.00 0.00 1.94
808 844 0.393820 AGTGGCCCGTCGAGTTAAAA 59.606 50.000 0.00 0.00 0.00 1.52
809 845 0.037975 GAGTGGCCCGTCGAGTTAAA 60.038 55.000 0.00 0.00 0.00 1.52
810 846 1.180456 TGAGTGGCCCGTCGAGTTAA 61.180 55.000 0.00 0.00 0.00 2.01
894 930 2.588877 CATCGTCATCCGGTGCCC 60.589 66.667 0.00 0.00 41.47 5.36
910 946 3.397439 GGGGAGCAGAGCAGAGCA 61.397 66.667 0.00 0.00 0.00 4.26
1008 1048 1.253100 TGGCGGTGGATTTCCTTTTC 58.747 50.000 0.00 0.00 36.82 2.29
1026 1066 1.662517 GTTTTGTTGGGGTTGGCTTG 58.337 50.000 0.00 0.00 0.00 4.01
1191 1261 3.040147 TGAAGCGAAGGAACTAACTGG 57.960 47.619 0.00 0.00 38.49 4.00
1193 1263 4.058817 CACTTGAAGCGAAGGAACTAACT 58.941 43.478 0.00 0.00 38.49 2.24
1201 1275 1.593196 TCCAACACTTGAAGCGAAGG 58.407 50.000 0.00 0.00 0.00 3.46
1238 1312 1.227674 CAACCCGCCCTGATCTAGC 60.228 63.158 0.00 0.00 0.00 3.42
1240 1314 2.908015 GCAACCCGCCCTGATCTA 59.092 61.111 0.00 0.00 32.94 1.98
1274 1354 3.986996 ATCCAAAATCCAAAAGCCAGG 57.013 42.857 0.00 0.00 0.00 4.45
1278 1358 4.388485 ACACCAATCCAAAATCCAAAAGC 58.612 39.130 0.00 0.00 0.00 3.51
1279 1359 5.277925 GCAACACCAATCCAAAATCCAAAAG 60.278 40.000 0.00 0.00 0.00 2.27
1330 1412 7.589574 CATCATTTGCTGAATGTGAAATTCA 57.410 32.000 0.00 0.00 44.46 2.57
1359 1441 0.530744 CACGCCTGCCTGTAACTCTA 59.469 55.000 0.00 0.00 0.00 2.43
1401 1487 7.627311 AGAGGAAACAAAATATACGGGTTAGT 58.373 34.615 0.00 0.00 0.00 2.24
1413 1499 3.690460 AGCATCGGAGAGGAAACAAAAT 58.310 40.909 0.00 0.00 43.16 1.82
1421 1507 2.151502 AGAAGAAGCATCGGAGAGGA 57.848 50.000 0.00 0.00 43.16 3.71
1606 1693 6.005823 TGTTTGAACTGGATCTGATGACAAT 58.994 36.000 0.00 0.00 0.00 2.71
1609 1696 4.999950 ACTGTTTGAACTGGATCTGATGAC 59.000 41.667 0.00 0.00 32.82 3.06
1627 1714 7.901029 TCTCTGAGTTATCATTCAGAACTGTT 58.099 34.615 4.32 0.00 46.53 3.16
1629 1716 6.476380 GCTCTCTGAGTTATCATTCAGAACTG 59.524 42.308 4.32 0.00 46.53 3.16
1639 1726 5.114780 GCAGATTTGCTCTCTGAGTTATCA 58.885 41.667 12.87 0.00 46.95 2.15
1681 1769 2.738314 GCAGCTTTGTTGCTAAAATGGG 59.262 45.455 0.00 0.00 41.98 4.00
1723 1815 6.099159 AGGTAACCTTACTGTCTCTGTTTC 57.901 41.667 0.00 0.00 34.16 2.78
1737 1829 4.041321 GGTCTCAACTGGTAAGGTAACCTT 59.959 45.833 0.00 0.00 46.63 3.50
1740 1832 4.566987 CAGGTCTCAACTGGTAAGGTAAC 58.433 47.826 0.00 0.00 32.38 2.50
1741 1833 3.007614 GCAGGTCTCAACTGGTAAGGTAA 59.992 47.826 0.00 0.00 36.48 2.85
1742 1834 2.565834 GCAGGTCTCAACTGGTAAGGTA 59.434 50.000 0.00 0.00 36.48 3.08
1743 1835 1.348036 GCAGGTCTCAACTGGTAAGGT 59.652 52.381 0.00 0.00 36.48 3.50
1744 1836 1.673033 CGCAGGTCTCAACTGGTAAGG 60.673 57.143 0.00 0.00 36.48 2.69
1745 1837 1.272490 TCGCAGGTCTCAACTGGTAAG 59.728 52.381 0.00 0.00 36.48 2.34
1747 1839 0.601558 GTCGCAGGTCTCAACTGGTA 59.398 55.000 0.00 0.00 36.48 3.25
1761 1855 0.939106 CGCATCGATACCATGTCGCA 60.939 55.000 0.00 0.00 38.88 5.10
1953 2047 2.579787 CTGCCGGAGTAGCGAACG 60.580 66.667 5.05 0.00 0.00 3.95
2019 2113 1.555075 TGAGTACAATGGCAGTCCTCC 59.445 52.381 0.00 0.00 0.00 4.30
2047 2141 2.871022 CAGTATGAGGCTGCTGTCATTC 59.129 50.000 18.60 14.82 39.69 2.67
2081 2175 6.155827 TGTCTTCCTCAACAACAACAAAAAG 58.844 36.000 0.00 0.00 0.00 2.27
2134 2231 3.389329 AGGTCGATACTGAGATGCCAATT 59.611 43.478 0.00 0.00 0.00 2.32
2147 2244 8.534333 TTGCTTATGATAATTCAGGTCGATAC 57.466 34.615 0.00 0.00 34.73 2.24
2152 2249 6.874288 AGCTTGCTTATGATAATTCAGGTC 57.126 37.500 0.00 0.00 34.73 3.85
2154 2251 9.622004 CAAATAGCTTGCTTATGATAATTCAGG 57.378 33.333 0.00 0.00 34.73 3.86
2184 2281 5.217393 CACCAGCAATTTTCCGATCATATG 58.783 41.667 0.00 0.00 0.00 1.78
2185 2282 4.261741 GCACCAGCAATTTTCCGATCATAT 60.262 41.667 0.00 0.00 41.58 1.78
2414 2511 5.162637 TCATAGGGTAGCTTGGGTATGAAT 58.837 41.667 0.00 0.00 0.00 2.57
2444 2541 3.486108 CGTAATTGTCATAGTCAGTCGCC 59.514 47.826 0.00 0.00 0.00 5.54
2605 2702 5.465390 TCAGAACGTTAGGTGATTTCAACAG 59.535 40.000 0.00 0.00 35.62 3.16
2613 2710 3.055819 AGTGCATCAGAACGTTAGGTGAT 60.056 43.478 15.42 13.80 0.00 3.06
2623 2720 3.999001 TCAGATCACAAGTGCATCAGAAC 59.001 43.478 0.00 0.00 0.00 3.01
2624 2721 4.276058 TCAGATCACAAGTGCATCAGAA 57.724 40.909 0.00 0.00 0.00 3.02
2636 2733 6.317140 GGCAGACAGATTATTTTCAGATCACA 59.683 38.462 0.00 0.00 0.00 3.58
2653 2751 0.394192 TCTGGTTCAGTGGCAGACAG 59.606 55.000 0.00 0.00 32.61 3.51
2660 2759 6.471233 TCTTGAGTATATCTGGTTCAGTGG 57.529 41.667 0.00 0.00 32.61 4.00
2695 2794 1.475403 TCTCGATGAACTCTGGTCCC 58.525 55.000 0.00 0.00 0.00 4.46
2701 2800 5.391097 CGACTTGTACTTCTCGATGAACTCT 60.391 44.000 0.00 0.00 0.00 3.24
2749 2849 2.353109 CGTGTCCTTGATCTTGCTCAGA 60.353 50.000 0.00 0.00 35.33 3.27
2751 2851 1.941209 GCGTGTCCTTGATCTTGCTCA 60.941 52.381 0.00 0.00 0.00 4.26
2827 2927 2.273449 GTCAGGGCCTGGTCCATG 59.727 66.667 32.23 16.65 39.13 3.66
2961 4674 0.320683 CACCGATCAGTGGAACAGCA 60.321 55.000 0.76 0.00 41.80 4.41
3011 4724 8.424918 TGAAGGGATCTACTTAGATTTGTCATC 58.575 37.037 0.28 0.00 42.79 2.92
3016 4729 6.989169 CCACTGAAGGGATCTACTTAGATTTG 59.011 42.308 0.28 0.00 42.79 2.32
3021 4734 3.964031 AGCCACTGAAGGGATCTACTTAG 59.036 47.826 3.70 5.14 0.00 2.18
3053 4766 4.023291 GTCCTCCAATAGATTTTTGGGCA 58.977 43.478 2.84 0.00 43.19 5.36
3077 4790 7.390162 TGTTTTGAGAATGTATCATGTGCACTA 59.610 33.333 19.41 4.84 0.00 2.74
3078 4791 6.207221 TGTTTTGAGAATGTATCATGTGCACT 59.793 34.615 19.41 0.00 0.00 4.40
3085 4798 7.984050 ACGAGAGATGTTTTGAGAATGTATCAT 59.016 33.333 0.00 0.00 0.00 2.45
3092 4805 6.279513 AGAGACGAGAGATGTTTTGAGAAT 57.720 37.500 0.00 0.00 0.00 2.40
3099 4812 6.239176 GGATGGAATAGAGACGAGAGATGTTT 60.239 42.308 0.00 0.00 0.00 2.83
3105 4818 3.491342 TGGGATGGAATAGAGACGAGAG 58.509 50.000 0.00 0.00 0.00 3.20
3110 4823 5.294552 CGTTTCTTTGGGATGGAATAGAGAC 59.705 44.000 0.00 0.00 0.00 3.36
3117 4830 1.611491 GTGCGTTTCTTTGGGATGGAA 59.389 47.619 0.00 0.00 0.00 3.53
3133 4846 8.958229 TTGTAAACAAAAATAAAATTCGTGCG 57.042 26.923 0.00 0.00 32.11 5.34
3150 4863 9.778741 AGAGATACTGAACATCTTTTGTAAACA 57.221 29.630 0.00 0.00 37.68 2.83
3152 4865 9.996554 TGAGAGATACTGAACATCTTTTGTAAA 57.003 29.630 0.00 0.00 37.68 2.01
3153 4866 9.424319 GTGAGAGATACTGAACATCTTTTGTAA 57.576 33.333 0.00 0.00 37.68 2.41
3154 4867 8.585018 TGTGAGAGATACTGAACATCTTTTGTA 58.415 33.333 0.00 0.00 37.68 2.41
3155 4868 7.386299 GTGTGAGAGATACTGAACATCTTTTGT 59.614 37.037 0.00 0.00 41.53 2.83
3156 4869 7.601886 AGTGTGAGAGATACTGAACATCTTTTG 59.398 37.037 0.00 0.00 32.86 2.44
3157 4870 7.675062 AGTGTGAGAGATACTGAACATCTTTT 58.325 34.615 0.00 0.00 32.86 2.27
3158 4871 7.238486 AGTGTGAGAGATACTGAACATCTTT 57.762 36.000 0.00 0.00 32.86 2.52
3159 4872 6.849085 AGTGTGAGAGATACTGAACATCTT 57.151 37.500 0.00 0.00 32.86 2.40
3165 4878 9.261180 CAAACTTTTAGTGTGAGAGATACTGAA 57.739 33.333 0.00 0.00 35.43 3.02
3169 4882 8.827677 ACAACAAACTTTTAGTGTGAGAGATAC 58.172 33.333 4.09 0.00 35.43 2.24
3207 4920 9.722056 GTCATGTGACAAGGAATTTGAATATAC 57.278 33.333 8.22 0.00 44.18 1.47
3336 5049 6.381801 GTGTTTGAAATGTATCCCAAGACTG 58.618 40.000 0.00 0.00 0.00 3.51
3380 5093 8.912988 TGAAAAGGTTGAGTGAAATAAATGACT 58.087 29.630 0.00 0.00 0.00 3.41
3381 5094 9.185192 CTGAAAAGGTTGAGTGAAATAAATGAC 57.815 33.333 0.00 0.00 0.00 3.06
3382 5095 8.912988 ACTGAAAAGGTTGAGTGAAATAAATGA 58.087 29.630 0.00 0.00 29.13 2.57
3408 5121 9.066892 AGCTTGACAAATAAGAAGTTTCACATA 57.933 29.630 0.00 0.00 0.00 2.29
3409 5122 7.864379 CAGCTTGACAAATAAGAAGTTTCACAT 59.136 33.333 0.00 0.00 0.00 3.21
3517 5230 9.934190 GAATGAAATAAGCAACAACACAAAAAT 57.066 25.926 0.00 0.00 0.00 1.82
3522 5237 8.659925 AAATGAATGAAATAAGCAACAACACA 57.340 26.923 0.00 0.00 0.00 3.72
3524 5239 8.883954 TGAAATGAATGAAATAAGCAACAACA 57.116 26.923 0.00 0.00 0.00 3.33
3531 5246 9.977762 GGTGAAATTGAAATGAATGAAATAAGC 57.022 29.630 0.00 0.00 0.00 3.09
3885 5600 9.599866 TGTTGAATTCACTCATTCTATAATCGT 57.400 29.630 7.89 0.00 34.66 3.73


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

AutoCloner maintained by Alex Coulton.