Multiple sequence alignment - TraesCS3A01G372300

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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 TraesCS3A01G372300 chr3A 100.000 3954 0 0 846 4799 623036196 623040149 0.000000e+00 7302.0
1 TraesCS3A01G372300 chr3A 100.000 460 0 0 1 460 623035351 623035810 0.000000e+00 850.0
2 TraesCS3A01G372300 chr3B 92.607 2002 102 14 846 2830 640056156 640058128 0.000000e+00 2835.0
3 TraesCS3A01G372300 chr3B 91.970 1980 97 21 2835 4778 640058508 640060461 0.000000e+00 2719.0
4 TraesCS3A01G372300 chr3B 91.026 312 17 7 154 460 640055576 640055881 1.240000e-110 411.0
5 TraesCS3A01G372300 chr3B 89.286 224 17 6 2621 2839 640058236 640058457 1.700000e-69 274.0
6 TraesCS3A01G372300 chr3B 88.811 143 11 3 1932 2070 640057069 640057210 2.300000e-38 171.0
7 TraesCS3A01G372300 chr3B 85.802 162 17 4 1765 1925 640057222 640057378 2.970000e-37 167.0
8 TraesCS3A01G372300 chr3D 92.538 1970 104 20 2835 4779 479610562 479612513 0.000000e+00 2784.0
9 TraesCS3A01G372300 chr3D 93.818 1844 78 15 856 2681 479608309 479610134 0.000000e+00 2741.0
10 TraesCS3A01G372300 chr3D 92.720 261 7 7 202 460 479607706 479607956 2.730000e-97 366.0
11 TraesCS3A01G372300 chr3D 93.750 208 10 3 1 205 479607046 479607253 4.660000e-80 309.0
12 TraesCS3A01G372300 chr3D 88.991 218 12 2 2621 2836 479610305 479610512 4.760000e-65 259.0
13 TraesCS3A01G372300 chr3D 87.037 162 16 3 1765 1925 479609384 479609541 1.370000e-40 178.0
14 TraesCS3A01G372300 chr3D 88.060 67 8 0 5 71 577147820 577147886 3.980000e-11 80.5
15 TraesCS3A01G372300 chr1A 88.732 71 8 0 2 72 454031512 454031582 2.380000e-13 87.9
16 TraesCS3A01G372300 chr7B 87.324 71 6 2 6 75 714839755 714839687 1.430000e-10 78.7
17 TraesCS3A01G372300 chr7D 89.474 57 3 2 2548 2604 254897205 254897152 8.620000e-08 69.4
18 TraesCS3A01G372300 chr2B 83.333 72 12 0 1 72 5764818 5764747 3.100000e-07 67.6


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 TraesCS3A01G372300 chr3A 623035351 623040149 4798 False 4076.000000 7302 100.000000 1 4799 2 chr3A.!!$F1 4798
1 TraesCS3A01G372300 chr3B 640055576 640060461 4885 False 1096.166667 2835 89.917000 154 4778 6 chr3B.!!$F1 4624
2 TraesCS3A01G372300 chr3D 479607046 479612513 5467 False 1106.166667 2784 91.475667 1 4779 6 chr3D.!!$F2 4778

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
327 787 0.041312 CGTTCGTTCTGCTTTGGTGG 60.041 55.0 0.00 0.00 0.00 4.61 F
1383 1996 0.179156 CCGCAGTCATTGATTGCACC 60.179 55.0 27.11 5.39 43.81 5.01 F
2930 3962 0.041238 TGTGGACTCGAGGGGAGAAT 59.959 55.0 18.41 0.00 46.23 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 2760 1.418637 AGTCTAAACCAGGCCAAACGA 59.581 47.619 5.01 0.0 0.0 3.85 R
2974 4006 0.397941 CAAGAAGGTCCAGTCAGCCA 59.602 55.000 0.00 0.0 0.0 4.75 R
4779 5844 0.527565 ACCGCTGATGAAAATGTGCC 59.472 50.000 0.00 0.0 0.0 5.01 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
39 40 3.389925 AGGTGGACATTTTGCATGTTG 57.610 42.857 0.00 0.00 31.52 3.33
64 65 8.378565 TGAGAGAATTGAGACCAACTTCTTAAT 58.621 33.333 0.00 0.00 34.23 1.40
195 199 1.986631 TCCCCTTCGGTGTCCAAATTA 59.013 47.619 0.00 0.00 0.00 1.40
198 202 4.414182 TCCCCTTCGGTGTCCAAATTATAT 59.586 41.667 0.00 0.00 0.00 0.86
250 710 2.345641 CGAATGCAGACGAGAACGAAAT 59.654 45.455 9.22 0.00 42.66 2.17
251 711 3.540359 CGAATGCAGACGAGAACGAAATC 60.540 47.826 9.22 0.00 42.66 2.17
252 712 2.724977 TGCAGACGAGAACGAAATCT 57.275 45.000 0.00 0.00 42.66 2.40
253 713 2.328473 TGCAGACGAGAACGAAATCTG 58.672 47.619 0.00 0.00 40.56 2.90
255 715 2.328473 CAGACGAGAACGAAATCTGCA 58.672 47.619 0.00 0.00 42.66 4.41
256 716 2.343843 CAGACGAGAACGAAATCTGCAG 59.656 50.000 7.63 7.63 42.66 4.41
259 719 3.131396 ACGAGAACGAAATCTGCAGTTT 58.869 40.909 14.67 13.20 42.66 2.66
260 720 4.304110 ACGAGAACGAAATCTGCAGTTTA 58.696 39.130 14.67 0.00 42.66 2.01
261 721 4.150098 ACGAGAACGAAATCTGCAGTTTAC 59.850 41.667 14.67 3.83 42.66 2.01
267 727 4.620184 ACGAAATCTGCAGTTTACTACGTC 59.380 41.667 14.67 4.29 0.00 4.34
323 783 4.099924 CGCGTTCGTTCTGCTTTG 57.900 55.556 0.00 0.00 0.00 2.77
324 784 1.438710 CGCGTTCGTTCTGCTTTGG 60.439 57.895 0.00 0.00 0.00 3.28
325 785 1.647084 GCGTTCGTTCTGCTTTGGT 59.353 52.632 0.00 0.00 0.00 3.67
327 787 0.041312 CGTTCGTTCTGCTTTGGTGG 60.041 55.000 0.00 0.00 0.00 4.61
328 788 1.305201 GTTCGTTCTGCTTTGGTGGA 58.695 50.000 0.00 0.00 0.00 4.02
428 892 3.291101 TTTCTTCCCGTCGGCCGAG 62.291 63.158 31.97 21.83 39.56 4.63
429 893 4.728110 TCTTCCCGTCGGCCGAGA 62.728 66.667 31.97 20.47 39.56 4.04
894 1502 4.150451 CAGCAATTTGATTTGTTCGAACCC 59.850 41.667 24.78 11.97 30.32 4.11
934 1543 5.278061 TCTTAGCTGGAACTGGGTACTATT 58.722 41.667 0.00 0.00 0.00 1.73
995 1607 1.215423 AGGGTTCAGTTGAAGGCTTGT 59.785 47.619 3.46 0.00 34.27 3.16
997 1609 1.338020 GGTTCAGTTGAAGGCTTGTGG 59.662 52.381 3.46 0.00 34.27 4.17
1005 1618 1.000396 AAGGCTTGTGGAGATGGGC 60.000 57.895 0.00 0.00 0.00 5.36
1038 1651 1.611673 CGGTTGATTGGACTGAAGGCT 60.612 52.381 0.00 0.00 0.00 4.58
1087 1700 1.838112 TCATGGACTGGGCATGAAAC 58.162 50.000 0.00 0.00 33.05 2.78
1096 1709 1.005097 TGGGCATGAAACTGCTCTCAT 59.995 47.619 0.00 0.00 43.32 2.90
1374 1987 0.606401 CTGGTGAACCCGCAGTCATT 60.606 55.000 0.00 0.00 35.15 2.57
1383 1996 0.179156 CCGCAGTCATTGATTGCACC 60.179 55.000 27.11 5.39 43.81 5.01
1413 2026 5.609423 CTGCCAAGAAGCTCAACTATATCT 58.391 41.667 0.00 0.00 0.00 1.98
1561 2174 9.169592 GTGCCTATGGTAAGTTTTTATCTGTTA 57.830 33.333 0.00 0.00 0.00 2.41
1562 2175 9.391006 TGCCTATGGTAAGTTTTTATCTGTTAG 57.609 33.333 0.00 0.00 0.00 2.34
1672 2288 7.492669 TGAATTCACTTATGCAGCTTACTACTC 59.507 37.037 3.38 0.00 0.00 2.59
1674 2290 5.651530 TCACTTATGCAGCTTACTACTCAC 58.348 41.667 0.00 0.00 0.00 3.51
1743 2360 6.149308 TGGATAAACTGTTGAGCTGTATTGTG 59.851 38.462 0.00 0.00 0.00 3.33
1776 2394 1.955778 TGCATTTCTGTCCTGTGGTTG 59.044 47.619 0.00 0.00 0.00 3.77
1778 2396 2.030805 GCATTTCTGTCCTGTGGTTGTC 60.031 50.000 0.00 0.00 0.00 3.18
1797 2415 7.094377 TGGTTGTCCTTAGCATTTCTGATTTAC 60.094 37.037 0.00 0.00 34.23 2.01
1803 2421 7.888021 TCCTTAGCATTTCTGATTTACCTTTCA 59.112 33.333 0.00 0.00 0.00 2.69
1836 2454 6.426937 TCAAAGTTAAACTGCCTCTCATACAC 59.573 38.462 0.00 0.00 0.00 2.90
1925 2543 2.287970 CCATATGCGCGACTACAAGGTA 60.288 50.000 12.10 0.00 0.00 3.08
1930 2548 0.742505 CGCGACTACAAGGTATCCCA 59.257 55.000 0.00 0.00 0.00 4.37
1997 2615 9.079833 CAAAATTAAACTGCCTCTCATACATTG 57.920 33.333 0.00 0.00 0.00 2.82
1998 2616 8.579850 AAATTAAACTGCCTCTCATACATTGA 57.420 30.769 0.00 0.00 0.00 2.57
2001 2619 5.426689 AACTGCCTCTCATACATTGAAGA 57.573 39.130 0.00 0.00 32.78 2.87
2070 2688 4.777896 AGGTCAAGATATACCCATATGCGT 59.222 41.667 0.00 0.00 36.34 5.24
2073 2691 6.341316 GTCAAGATATACCCATATGCGTGAT 58.659 40.000 3.19 0.00 0.00 3.06
2086 2704 1.950216 TGCGTGATTACAAGGTTTGCA 59.050 42.857 0.00 0.00 0.00 4.08
2139 2757 5.882000 TGTAATGTCATCCATTGTCTCAAGG 59.118 40.000 0.00 0.00 43.63 3.61
2142 2760 1.918262 TCATCCATTGTCTCAAGGGCT 59.082 47.619 8.09 0.00 0.00 5.19
2298 2918 6.525629 AGTTGTGTGTATTGAGCTCTTAGTT 58.474 36.000 16.19 0.00 0.00 2.24
2323 2943 5.697633 CCAATAGCATGCCCATTTGAATAAC 59.302 40.000 15.66 0.00 0.00 1.89
2352 2972 8.986929 AGGTTAGTACAATAGTTATAGACGGT 57.013 34.615 0.00 0.00 0.00 4.83
2362 2982 2.745281 GTTATAGACGGTTTTGCAGCCA 59.255 45.455 0.00 0.00 0.00 4.75
2493 3123 4.747265 AAACAGCCATATGGGGATACAT 57.253 40.909 23.30 0.00 37.04 2.29
2502 3132 6.738731 GCCATATGGGGATACATCGTGTATAG 60.739 46.154 23.30 0.00 39.32 1.31
2506 3136 6.280855 TGGGGATACATCGTGTATAGATTG 57.719 41.667 9.61 0.00 43.08 2.67
2507 3137 6.014012 TGGGGATACATCGTGTATAGATTGA 58.986 40.000 9.61 0.00 43.08 2.57
2508 3138 6.495526 TGGGGATACATCGTGTATAGATTGAA 59.504 38.462 9.61 0.00 43.08 2.69
2509 3139 7.015779 TGGGGATACATCGTGTATAGATTGAAA 59.984 37.037 9.61 0.00 43.08 2.69
2510 3140 7.876068 GGGGATACATCGTGTATAGATTGAAAA 59.124 37.037 9.61 0.00 43.08 2.29
2511 3141 9.268268 GGGATACATCGTGTATAGATTGAAAAA 57.732 33.333 9.61 0.00 43.08 1.94
2696 3656 9.944376 ACCATATGCTAGTATTACAACATAAGG 57.056 33.333 15.80 15.80 35.83 2.69
2699 3659 5.294356 TGCTAGTATTACAACATAAGGCCG 58.706 41.667 0.00 0.00 0.00 6.13
2701 3661 3.128349 AGTATTACAACATAAGGCCGCG 58.872 45.455 0.00 0.00 0.00 6.46
2780 3740 2.593725 CCCCAGATGCCATGCTCG 60.594 66.667 0.00 0.00 0.00 5.03
2781 3741 2.593725 CCCAGATGCCATGCTCGG 60.594 66.667 0.00 0.00 0.00 4.63
2796 3756 1.537135 GCTCGGTAGCTAGCAAGAAGG 60.537 57.143 21.99 5.44 45.85 3.46
2797 3757 1.067821 CTCGGTAGCTAGCAAGAAGGG 59.932 57.143 21.99 2.15 0.00 3.95
2859 3879 0.718343 CGTACTTTGCTGCTGAGAGC 59.282 55.000 0.00 0.00 42.82 4.09
2877 3897 1.598701 GCAAAGCTGGCCGGAGATTT 61.599 55.000 18.31 8.29 31.76 2.17
2923 3955 0.460987 GCAGGAATGTGGACTCGAGG 60.461 60.000 18.41 0.00 0.00 4.63
2930 3962 0.041238 TGTGGACTCGAGGGGAGAAT 59.959 55.000 18.41 0.00 46.23 2.40
2949 3981 1.109920 TAGGAGATGGGCTGCTCGAC 61.110 60.000 0.00 0.00 42.15 4.20
2971 4003 4.161754 ACTGATGCCTGTTAGGGTTAGTAC 59.838 45.833 0.00 0.00 35.37 2.73
2974 4006 5.190925 TGATGCCTGTTAGGGTTAGTACATT 59.809 40.000 0.00 0.00 35.37 2.71
2992 4024 1.140312 TTGGCTGACTGGACCTTCTT 58.860 50.000 0.00 0.00 0.00 2.52
3130 4178 2.005971 GGATACCGCGACTTTTGACT 57.994 50.000 8.23 0.00 0.00 3.41
3206 4254 7.334171 GCATTACAGTTTTGGCATTTTCCTATT 59.666 33.333 0.00 0.00 0.00 1.73
3314 4362 6.285990 TGTCCTTTTCACAACTAGGAAGTAC 58.714 40.000 0.00 0.00 38.46 2.73
3379 4427 4.550076 AAAGAGCATCAGTGAAGTAGCT 57.450 40.909 11.10 11.10 37.82 3.32
3396 4444 9.456147 TGAAGTAGCTTGTAAATTAGCCATTAA 57.544 29.630 0.00 0.00 0.00 1.40
3404 4452 8.925161 TTGTAAATTAGCCATTAAGTTGATGC 57.075 30.769 2.13 0.00 32.35 3.91
3508 4556 5.163195 ACAGAGAGCAAAGTTTCCTTTCCTA 60.163 40.000 0.00 0.00 38.87 2.94
3554 4602 5.120208 TCGTCATCTAAGTGCTTTGCTAAAC 59.880 40.000 0.00 0.00 0.00 2.01
3603 4651 3.059884 CGTGATGTGTGCACTTCTAGTT 58.940 45.455 19.41 0.00 36.70 2.24
3606 4654 1.217001 TGTGTGCACTTCTAGTTGCG 58.783 50.000 19.41 0.00 0.00 4.85
3871 4919 6.941857 TCATGCTTTGGTGTTATCTACTGTA 58.058 36.000 0.00 0.00 0.00 2.74
3958 5006 7.488471 GGATACGTGGATATTCTATTACTGTGC 59.512 40.741 0.00 0.00 0.00 4.57
3993 5041 7.395190 TGCTCTTTTTATGCATACTGTTCAT 57.605 32.000 5.74 0.00 0.00 2.57
4083 5134 1.510776 CTGCTAGCCTGCTAGATTGC 58.489 55.000 26.17 14.06 46.56 3.56
4108 5162 6.645415 CCATTTATAACGGAGTGTATGTCTCC 59.355 42.308 2.27 2.27 45.00 3.71
4119 5173 2.091499 TGTATGTCTCCCATCCGTACCT 60.091 50.000 0.00 0.00 34.86 3.08
4120 5174 2.176247 ATGTCTCCCATCCGTACCTT 57.824 50.000 0.00 0.00 0.00 3.50
4156 5210 5.051891 GCAGTACCATGCATTCAATATCC 57.948 43.478 0.00 0.00 45.77 2.59
4219 5281 3.837213 TTCATAGCTTTCTTGTGCTGC 57.163 42.857 0.00 0.00 40.08 5.25
4251 5313 6.256104 CCGTCGTGTAACCATTTCATTATGTA 59.744 38.462 0.00 0.00 0.00 2.29
4298 5360 7.252612 TCCTGACTTACCTATGTTGATTGAA 57.747 36.000 0.00 0.00 0.00 2.69
4420 5482 6.271391 TCCTTTTTACCATCTGTCTGTCCTTA 59.729 38.462 0.00 0.00 0.00 2.69
4437 5499 4.816925 GTCCTTATTAATGAGCGGCTTTCT 59.183 41.667 2.97 0.00 0.00 2.52
4446 5508 2.427453 TGAGCGGCTTTCTAGTTAGAGG 59.573 50.000 2.97 0.00 33.21 3.69
4466 5528 2.527100 GTTGAATTCTGAGCTGCATGC 58.473 47.619 11.82 11.82 43.29 4.06
4488 5550 6.834107 TGCTTGGAATGATCTTCATCTGATA 58.166 36.000 0.00 0.00 35.76 2.15
4492 5554 6.465084 TGGAATGATCTTCATCTGATAGCAG 58.535 40.000 0.24 0.24 43.67 4.24
4502 5564 1.550524 TCTGATAGCAGGTTTCACGCT 59.449 47.619 8.37 0.00 42.53 5.07
4614 5679 9.846248 GCTGTTTCTTTTACATCTGTTTATCAT 57.154 29.630 0.00 0.00 0.00 2.45
4693 5758 7.589395 TGTTTCGACATGTATTGCTTAACATT 58.411 30.769 0.00 0.00 34.12 2.71
4730 5795 5.836347 ACTGCTTCTTTCATGGTTTCTTTC 58.164 37.500 0.00 0.00 0.00 2.62
4761 5826 6.857964 ACAATTCGCTGATTGTTTCTAAAGTG 59.142 34.615 8.28 0.00 45.38 3.16
4774 5839 3.808728 TCTAAAGTGCTGCTGACTTGTT 58.191 40.909 6.18 0.00 33.85 2.83
4779 5844 1.003116 GTGCTGCTGACTTGTTCTGTG 60.003 52.381 0.00 0.00 0.00 3.66
4780 5845 0.590195 GCTGCTGACTTGTTCTGTGG 59.410 55.000 0.00 0.00 0.00 4.17
4781 5846 0.590195 CTGCTGACTTGTTCTGTGGC 59.410 55.000 0.00 0.00 0.00 5.01
4782 5847 0.107263 TGCTGACTTGTTCTGTGGCA 60.107 50.000 0.00 0.00 0.00 4.92
4783 5848 0.308993 GCTGACTTGTTCTGTGGCAC 59.691 55.000 11.55 11.55 0.00 5.01
4784 5849 1.667236 CTGACTTGTTCTGTGGCACA 58.333 50.000 20.76 20.76 0.00 4.57
4785 5850 2.224606 CTGACTTGTTCTGTGGCACAT 58.775 47.619 22.35 3.70 44.52 3.21
4786 5851 2.620115 CTGACTTGTTCTGTGGCACATT 59.380 45.455 22.35 0.00 44.52 2.71
4787 5852 3.023119 TGACTTGTTCTGTGGCACATTT 58.977 40.909 22.35 0.14 44.52 2.32
4788 5853 3.446873 TGACTTGTTCTGTGGCACATTTT 59.553 39.130 22.35 1.26 44.52 1.82
4789 5854 4.044426 GACTTGTTCTGTGGCACATTTTC 58.956 43.478 22.35 12.21 44.52 2.29
4790 5855 3.446873 ACTTGTTCTGTGGCACATTTTCA 59.553 39.130 22.35 14.55 44.52 2.69
4791 5856 4.099881 ACTTGTTCTGTGGCACATTTTCAT 59.900 37.500 22.35 1.62 44.52 2.57
4792 5857 4.241590 TGTTCTGTGGCACATTTTCATC 57.758 40.909 22.35 8.20 44.52 2.92
4793 5858 3.635836 TGTTCTGTGGCACATTTTCATCA 59.364 39.130 22.35 10.54 44.52 3.07
4794 5859 4.232221 GTTCTGTGGCACATTTTCATCAG 58.768 43.478 22.35 6.07 44.52 2.90
4795 5860 2.229543 TCTGTGGCACATTTTCATCAGC 59.770 45.455 22.35 0.00 44.52 4.26
4796 5861 1.068402 TGTGGCACATTTTCATCAGCG 60.068 47.619 17.96 0.00 44.52 5.18
4797 5862 0.527113 TGGCACATTTTCATCAGCGG 59.473 50.000 0.00 0.00 0.00 5.52
4798 5863 0.527565 GGCACATTTTCATCAGCGGT 59.472 50.000 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.387374 TCAACATGCAAAATGTCCACCTT 59.613 39.130 0.00 0.00 0.00 3.50
20 21 3.005684 TCTCAACATGCAAAATGTCCACC 59.994 43.478 0.00 0.00 0.00 4.61
39 40 8.785329 ATTAAGAAGTTGGTCTCAATTCTCTC 57.215 34.615 0.00 0.00 33.68 3.20
195 199 3.392616 CCCAGGTTCTTGCAGTAGGATAT 59.607 47.826 0.00 0.00 0.00 1.63
198 202 0.984230 CCCAGGTTCTTGCAGTAGGA 59.016 55.000 0.00 0.00 0.00 2.94
255 715 7.620458 GCTGGATGCTCAGACGTAGTAAACT 62.620 48.000 0.00 0.00 39.23 2.66
256 716 5.491279 GCTGGATGCTCAGACGTAGTAAAC 61.491 50.000 0.00 0.00 39.23 2.01
259 719 1.676529 GCTGGATGCTCAGACGTAGTA 59.323 52.381 0.00 0.00 39.23 1.82
260 720 0.457851 GCTGGATGCTCAGACGTAGT 59.542 55.000 0.00 0.00 41.38 2.73
261 721 0.249238 GGCTGGATGCTCAGACGTAG 60.249 60.000 0.00 0.00 42.39 3.51
316 776 2.634453 AGGGATTTTTCCACCAAAGCAG 59.366 45.455 0.00 0.00 0.00 4.24
323 783 2.097036 CGGGTTAGGGATTTTTCCACC 58.903 52.381 0.00 0.00 0.00 4.61
324 784 3.076079 TCGGGTTAGGGATTTTTCCAC 57.924 47.619 0.00 0.00 0.00 4.02
325 785 3.526019 AGATCGGGTTAGGGATTTTTCCA 59.474 43.478 0.00 0.00 0.00 3.53
327 787 7.634671 TTTTAGATCGGGTTAGGGATTTTTC 57.365 36.000 0.00 0.00 0.00 2.29
428 892 4.785453 CCCGGTGCTTCTGGCCTC 62.785 72.222 3.32 0.00 41.11 4.70
866 1366 2.063266 ACAAATCAAATTGCTGCGCAG 58.937 42.857 32.83 32.83 40.61 5.18
894 1502 3.528597 AAGAGGAAGCTACGCCTTTAG 57.471 47.619 4.41 0.00 33.84 1.85
934 1543 0.682852 ACAAACGTGAATCGGGAGGA 59.317 50.000 0.00 0.00 44.69 3.71
995 1607 1.984253 TATCCCCCAGCCCATCTCCA 61.984 60.000 0.00 0.00 0.00 3.86
997 1609 0.915364 GATATCCCCCAGCCCATCTC 59.085 60.000 0.00 0.00 0.00 2.75
1087 1700 0.183014 ATGAGGGGCAATGAGAGCAG 59.817 55.000 0.00 0.00 0.00 4.24
1096 1709 1.142870 GCAGGTGTATATGAGGGGCAA 59.857 52.381 0.00 0.00 0.00 4.52
1206 1819 2.359900 GAGAACATGACCCATGACCAC 58.640 52.381 13.22 2.85 43.81 4.16
1374 1987 2.036571 CAGCTCGCAGGTGCAATCA 61.037 57.895 2.33 0.00 42.21 2.57
1383 1996 3.036783 GCTTCTTGGCAGCTCGCAG 62.037 63.158 9.78 1.19 45.17 5.18
1413 2026 5.643348 AGCGACACACAAATATGAATTCTCA 59.357 36.000 7.05 0.00 35.56 3.27
1776 2394 7.631717 AAGGTAAATCAGAAATGCTAAGGAC 57.368 36.000 0.00 0.00 0.00 3.85
1778 2396 8.055279 TGAAAGGTAAATCAGAAATGCTAAGG 57.945 34.615 0.00 0.00 0.00 2.69
1925 2543 6.856757 AGAAATGCTAGAATAACCATGGGAT 58.143 36.000 18.09 6.11 0.00 3.85
1975 2593 8.049117 TCTTCAATGTATGAGAGGCAGTTTAAT 58.951 33.333 0.00 0.00 39.77 1.40
2070 2688 6.832520 ATGTATGTGCAAACCTTGTAATCA 57.167 33.333 0.00 0.00 0.00 2.57
2073 2691 6.427242 TCGTTATGTATGTGCAAACCTTGTAA 59.573 34.615 0.00 0.00 0.00 2.41
2127 2745 1.813513 AACGAGCCCTTGAGACAATG 58.186 50.000 0.00 0.00 0.00 2.82
2142 2760 1.418637 AGTCTAAACCAGGCCAAACGA 59.581 47.619 5.01 0.00 0.00 3.85
2245 2865 6.485830 TTCATAACCCAATTGAACAAACCA 57.514 33.333 7.12 0.00 0.00 3.67
2253 2873 8.865090 ACAACTTTGTATTCATAACCCAATTGA 58.135 29.630 7.12 0.00 40.16 2.57
2298 2918 3.029483 TCAAATGGGCATGCTATTGGA 57.971 42.857 18.92 17.33 0.00 3.53
2362 2982 7.625828 GGTAACTTAAACCTGAGTATTGCAT 57.374 36.000 0.00 0.00 33.97 3.96
2518 3148 8.984891 TCTTTCTGTTTTTATTACATGGCATG 57.015 30.769 25.31 25.31 0.00 4.06
2696 3656 3.130693 AGATCCTAAATATCCTACGCGGC 59.869 47.826 12.47 0.00 0.00 6.53
2699 3659 5.916661 TCCAGATCCTAAATATCCTACGC 57.083 43.478 0.00 0.00 0.00 4.42
2701 3661 9.268282 TGGTATTCCAGATCCTAAATATCCTAC 57.732 37.037 0.00 0.00 39.03 3.18
2780 3740 0.541863 TGCCCTTCTTGCTAGCTACC 59.458 55.000 17.23 0.00 0.00 3.18
2781 3741 1.657822 GTGCCCTTCTTGCTAGCTAC 58.342 55.000 17.23 0.00 0.00 3.58
2786 3746 1.002134 GCTGGTGCCCTTCTTGCTA 60.002 57.895 0.00 0.00 0.00 3.49
2796 3756 0.875059 GTCTTGTTACTGCTGGTGCC 59.125 55.000 0.00 0.00 38.71 5.01
2797 3757 1.532868 CTGTCTTGTTACTGCTGGTGC 59.467 52.381 0.00 0.00 40.20 5.01
2859 3879 0.453390 GAAATCTCCGGCCAGCTTTG 59.547 55.000 2.24 0.00 0.00 2.77
2877 3897 2.265739 GGCGCCTCTGACATGTGA 59.734 61.111 22.15 0.00 0.00 3.58
2923 3955 1.627834 CAGCCCATCTCCTATTCTCCC 59.372 57.143 0.00 0.00 0.00 4.30
2930 3962 1.109920 GTCGAGCAGCCCATCTCCTA 61.110 60.000 0.00 0.00 0.00 2.94
2949 3981 3.914426 ACTAACCCTAACAGGCATCAG 57.086 47.619 0.00 0.00 32.73 2.90
2971 4003 1.004044 AGAAGGTCCAGTCAGCCAATG 59.996 52.381 0.00 0.00 0.00 2.82
2974 4006 0.397941 CAAGAAGGTCCAGTCAGCCA 59.602 55.000 0.00 0.00 0.00 4.75
2992 4024 2.363975 GGGATACGCCAGGGACACA 61.364 63.158 0.00 0.00 38.95 3.72
3000 4032 3.340034 CTTAAACAACTGGGATACGCCA 58.660 45.455 0.00 0.00 38.95 5.69
3100 4148 4.583489 AGTCGCGGTATCCCCATATAATAG 59.417 45.833 6.13 0.00 0.00 1.73
3117 4165 3.328939 CGACAAGTCAAAAGTCGCG 57.671 52.632 0.00 0.00 46.74 5.87
3130 4178 4.060205 GTTTACCTAGAAAGCACCGACAA 58.940 43.478 0.00 0.00 0.00 3.18
3206 4254 7.567250 TGTCCTACATCATTTCTACCTTCCATA 59.433 37.037 0.00 0.00 0.00 2.74
3379 4427 8.526978 TGCATCAACTTAATGGCTAATTTACAA 58.473 29.630 0.00 0.00 0.00 2.41
3396 4444 1.684248 GGATCCTGCCTTGCATCAACT 60.684 52.381 3.84 0.00 38.13 3.16
3404 4452 0.529378 GCTGTTTGGATCCTGCCTTG 59.471 55.000 14.23 0.30 0.00 3.61
3508 4556 4.954092 GCTGTTAAGAGCTTAATGCACT 57.046 40.909 16.91 0.00 44.28 4.40
3554 4602 0.035152 TCTGCCATGGCCTGTTACAG 60.035 55.000 33.44 21.43 41.09 2.74
3603 4651 1.153369 GTCAGCTAATCCCAGCGCA 60.153 57.895 11.47 0.00 46.52 6.09
3606 4654 1.869767 CAATCGTCAGCTAATCCCAGC 59.130 52.381 0.00 0.00 42.12 4.85
3871 4919 3.844211 TGCCTTGGACATTTACTAGGACT 59.156 43.478 0.00 0.00 0.00 3.85
3958 5006 6.867816 TGCATAAAAAGAGCAACATTGTAAGG 59.132 34.615 0.00 0.00 34.97 2.69
3993 5041 3.824001 TTCAATGACCCCAAGGATCAA 57.176 42.857 0.00 0.00 36.73 2.57
4083 5134 6.645415 GGAGACATACACTCCGTTATAAATGG 59.355 42.308 0.00 0.00 43.25 3.16
4108 5162 3.866883 AAATGCAAAAGGTACGGATGG 57.133 42.857 0.00 0.00 0.00 3.51
4119 5173 5.918608 TGGTACTGCCTTAAAAATGCAAAA 58.081 33.333 0.00 0.00 38.35 2.44
4120 5174 5.537300 TGGTACTGCCTTAAAAATGCAAA 57.463 34.783 0.00 0.00 38.35 3.68
4219 5281 2.025418 GTTACACGACGGGCTGGTG 61.025 63.158 0.00 0.00 37.67 4.17
4251 5313 9.337396 AGGAAACTTCAAAACAAGAAACTTTTT 57.663 25.926 0.00 0.00 37.44 1.94
4256 5318 7.090808 AGTCAGGAAACTTCAAAACAAGAAAC 58.909 34.615 0.00 0.00 40.21 2.78
4298 5360 7.094634 CCAAAATGAGTACACTTCAGCATAACT 60.095 37.037 0.00 0.00 0.00 2.24
4387 5449 9.093458 AGACAGATGGTAAAAAGGATGAAAAAT 57.907 29.630 0.00 0.00 0.00 1.82
4420 5482 6.817184 TCTAACTAGAAAGCCGCTCATTAAT 58.183 36.000 0.00 0.00 0.00 1.40
4437 5499 6.634805 CAGCTCAGAATTCAACCTCTAACTA 58.365 40.000 8.44 0.00 0.00 2.24
4446 5508 2.527100 GCATGCAGCTCAGAATTCAAC 58.473 47.619 14.21 0.00 41.15 3.18
4466 5528 6.935208 TGCTATCAGATGAAGATCATTCCAAG 59.065 38.462 0.00 0.00 37.20 3.61
4488 5550 1.388547 TTTCAAGCGTGAAACCTGCT 58.611 45.000 21.60 0.00 46.48 4.24
4502 5564 3.753272 GCATCTAGCCAGAACTGTTTCAA 59.247 43.478 0.00 0.00 37.23 2.69
4532 5595 3.072184 ACTCAGGAACTCAACATCAGCTT 59.928 43.478 0.00 0.00 34.60 3.74
4614 5679 4.422073 ACAGAAGATGGAAGTTCACACA 57.578 40.909 5.01 0.00 0.00 3.72
4693 5758 7.228507 TGAAAGAAGCAGTAACATTTAAGAGCA 59.771 33.333 0.00 0.00 0.00 4.26
4730 5795 2.171567 CAATCAGCGAATTGTTGAGCG 58.828 47.619 6.07 0.00 41.39 5.03
4757 5822 1.945394 CAGAACAAGTCAGCAGCACTT 59.055 47.619 0.00 0.00 34.24 3.16
4761 5826 0.590195 CCACAGAACAAGTCAGCAGC 59.410 55.000 0.00 0.00 0.00 5.25
4774 5839 2.229543 GCTGATGAAAATGTGCCACAGA 59.770 45.455 3.00 0.00 0.00 3.41
4779 5844 0.527565 ACCGCTGATGAAAATGTGCC 59.472 50.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.