Multiple sequence alignment - TraesCS6A01G335900

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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 TraesCS6A01G335900 chr6A 100.000 4006 0 0 1 4006 568518944 568514939 0.000000e+00 7398
1 TraesCS6A01G335900 chr6D 92.795 3220 102 38 863 4006 423817013 423813848 0.000000e+00 4542
2 TraesCS6A01G335900 chr6B 94.688 2052 56 13 863 2887 639535056 639533031 0.000000e+00 3136
3 TraesCS6A01G335900 chr6B 90.652 460 23 10 2974 3418 639532990 639532536 9.590000e-166 593
4 TraesCS6A01G335900 chr6B 95.294 340 7 4 3428 3766 639531946 639531615 7.620000e-147 531
5 TraesCS6A01G335900 chr3A 93.894 868 49 4 1 866 623994200 623993335 0.000000e+00 1306
6 TraesCS6A01G335900 chr3A 92.644 870 57 4 1 866 451140616 451139750 0.000000e+00 1245
7 TraesCS6A01G335900 chr3A 92.546 872 59 4 1 866 584760656 584759785 0.000000e+00 1245
8 TraesCS6A01G335900 chr7A 93.403 864 54 3 1 861 661086722 661085859 0.000000e+00 1277
9 TraesCS6A01G335900 chr7A 93.279 863 56 2 1 861 33004876 33005738 0.000000e+00 1271
10 TraesCS6A01G335900 chr7A 93.056 144 10 0 1533 1676 121056642 121056785 1.130000e-50 211
11 TraesCS6A01G335900 chr7A 79.343 213 29 11 1197 1397 121056270 121056479 6.980000e-28 135
12 TraesCS6A01G335900 chr5A 92.734 867 61 2 1 865 502390571 502391437 0.000000e+00 1251
13 TraesCS6A01G335900 chr5A 92.529 870 62 3 1 868 679367620 679368488 0.000000e+00 1243
14 TraesCS6A01G335900 chr2A 92.841 866 57 4 1 861 755811838 755810973 0.000000e+00 1251
15 TraesCS6A01G335900 chr2A 89.552 134 14 0 1544 1677 687050274 687050407 1.910000e-38 171
16 TraesCS6A01G335900 chr5D 92.325 873 58 7 1 866 537321494 537320624 0.000000e+00 1232
17 TraesCS6A01G335900 chr7D 93.750 144 9 0 1533 1676 117133156 117133299 2.420000e-52 217
18 TraesCS6A01G335900 chr7D 81.183 186 24 9 1194 1372 117132790 117132971 5.400000e-29 139
19 TraesCS6A01G335900 chr7B 90.972 144 13 0 1533 1676 76904322 76904465 1.140000e-45 195
20 TraesCS6A01G335900 chr7B 81.538 195 22 10 1184 1372 76903937 76904123 8.970000e-32 148
21 TraesCS6A01G335900 chr2D 89.552 134 14 0 1544 1677 546209815 546209948 1.910000e-38 171
22 TraesCS6A01G335900 chr2B 89.552 134 14 0 1544 1677 653017848 653017981 1.910000e-38 171


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 TraesCS6A01G335900 chr6A 568514939 568518944 4005 True 7398 7398 100.000000 1 4006 1 chr6A.!!$R1 4005
1 TraesCS6A01G335900 chr6D 423813848 423817013 3165 True 4542 4542 92.795000 863 4006 1 chr6D.!!$R1 3143
2 TraesCS6A01G335900 chr6B 639531615 639535056 3441 True 1420 3136 93.544667 863 3766 3 chr6B.!!$R1 2903
3 TraesCS6A01G335900 chr3A 623993335 623994200 865 True 1306 1306 93.894000 1 866 1 chr3A.!!$R3 865
4 TraesCS6A01G335900 chr3A 451139750 451140616 866 True 1245 1245 92.644000 1 866 1 chr3A.!!$R1 865
5 TraesCS6A01G335900 chr3A 584759785 584760656 871 True 1245 1245 92.546000 1 866 1 chr3A.!!$R2 865
6 TraesCS6A01G335900 chr7A 661085859 661086722 863 True 1277 1277 93.403000 1 861 1 chr7A.!!$R1 860
7 TraesCS6A01G335900 chr7A 33004876 33005738 862 False 1271 1271 93.279000 1 861 1 chr7A.!!$F1 860
8 TraesCS6A01G335900 chr5A 502390571 502391437 866 False 1251 1251 92.734000 1 865 1 chr5A.!!$F1 864
9 TraesCS6A01G335900 chr5A 679367620 679368488 868 False 1243 1243 92.529000 1 868 1 chr5A.!!$F2 867
10 TraesCS6A01G335900 chr2A 755810973 755811838 865 True 1251 1251 92.841000 1 861 1 chr2A.!!$R1 860
11 TraesCS6A01G335900 chr5D 537320624 537321494 870 True 1232 1232 92.325000 1 866 1 chr5D.!!$R1 865

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
954 964 0.395862 CTCCTGCTTCCTCCGTCCTA 60.396 60.0 0.00 0.0 0.00 2.94 F
955 965 0.683504 TCCTGCTTCCTCCGTCCTAC 60.684 60.0 0.00 0.0 0.00 3.18 F
2886 2949 0.464452 GGTGGCGAGGCTACTATGTT 59.536 55.0 4.15 0.0 39.93 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2867 2930 0.464452 AACATAGTAGCCTCGCCACC 59.536 55.000 0.00 0.0 0.00 4.61 R
2945 3008 0.606401 CACAGGTGGTAGTGCAAGGG 60.606 60.000 0.00 0.0 0.00 3.95 R
3889 4558 1.589630 CTGCGGCCACAGTGTAGTA 59.410 57.895 12.88 0.0 32.78 1.82 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
162 163 2.350895 CCCAAGGATGGTCGTGCA 59.649 61.111 0.00 0.00 46.01 4.57
220 221 5.140177 GTGTTCATCAAGTGCTTAAACGAG 58.860 41.667 0.00 0.00 0.00 4.18
336 339 5.724370 TGGTATTGGGAAGAAGAGTACATCA 59.276 40.000 0.00 0.00 0.00 3.07
381 384 5.994887 AGTACATGTTCGTGCACTTTTAA 57.005 34.783 16.19 0.99 0.00 1.52
386 389 5.526111 ACATGTTCGTGCACTTTTAACTAGT 59.474 36.000 16.19 12.24 0.00 2.57
387 390 6.037830 ACATGTTCGTGCACTTTTAACTAGTT 59.962 34.615 16.19 13.68 0.00 2.24
390 393 8.145316 TGTTCGTGCACTTTTAACTAGTTTAT 57.855 30.769 14.49 0.00 0.00 1.40
460 463 2.808919 TGAGACTAGGTGTGAGGAAGG 58.191 52.381 0.00 0.00 0.00 3.46
530 533 4.566278 CCTCCTCCACAGATCAACAATGAA 60.566 45.833 0.00 0.00 39.49 2.57
579 583 1.272480 GGGGGCAGTTATGGAAGTTGT 60.272 52.381 0.00 0.00 0.00 3.32
775 785 1.302431 CACCGCATTCCAGGACACA 60.302 57.895 0.00 0.00 0.00 3.72
777 787 1.003355 CCGCATTCCAGGACACACT 60.003 57.895 0.00 0.00 0.00 3.55
784 794 0.541998 TCCAGGACACACTCGGACAT 60.542 55.000 0.00 0.00 0.00 3.06
785 795 1.182667 CCAGGACACACTCGGACATA 58.817 55.000 0.00 0.00 0.00 2.29
840 850 4.495019 CGAACAAAACAGACATCCGTTTGA 60.495 41.667 0.00 0.00 35.57 2.69
953 963 1.684049 CTCCTGCTTCCTCCGTCCT 60.684 63.158 0.00 0.00 0.00 3.85
954 964 0.395862 CTCCTGCTTCCTCCGTCCTA 60.396 60.000 0.00 0.00 0.00 2.94
955 965 0.683504 TCCTGCTTCCTCCGTCCTAC 60.684 60.000 0.00 0.00 0.00 3.18
956 966 0.684805 CCTGCTTCCTCCGTCCTACT 60.685 60.000 0.00 0.00 0.00 2.57
957 967 0.741915 CTGCTTCCTCCGTCCTACTC 59.258 60.000 0.00 0.00 0.00 2.59
958 968 0.683504 TGCTTCCTCCGTCCTACTCC 60.684 60.000 0.00 0.00 0.00 3.85
1001 1011 0.752054 CATCCTCAGAGAGTGCTCCC 59.248 60.000 0.00 0.00 42.30 4.30
1007 1017 1.305718 AGAGAGTGCTCCCCTCCAC 60.306 63.158 0.00 0.00 42.30 4.02
1416 1432 1.226746 CCGTGTCTTCTTCACCAACC 58.773 55.000 0.00 0.00 32.86 3.77
1422 1438 3.694072 TGTCTTCTTCACCAACCTGTTTG 59.306 43.478 0.00 0.00 34.63 2.93
1465 1481 1.202817 CCTTGCTTGCATGCATGTACA 59.797 47.619 28.20 18.62 42.96 2.90
1504 1520 2.551912 GGACGGTGTTGCAGTTGGG 61.552 63.158 0.00 0.00 0.00 4.12
1645 1661 2.743752 CGAGAAGCACATGCACCGG 61.744 63.158 0.00 0.00 45.16 5.28
1723 1739 2.581726 CTTCCTCCTCGGCCTCCTCT 62.582 65.000 0.00 0.00 0.00 3.69
1777 1793 4.525028 ACCACCACCACCTCCCCA 62.525 66.667 0.00 0.00 0.00 4.96
2061 2077 1.131504 CTTCTTCTCCTCCGACGTCAG 59.868 57.143 17.16 3.99 0.00 3.51
2263 2303 2.660064 GGAGAAGGAGAGGCGGCAA 61.660 63.158 13.08 0.00 0.00 4.52
2389 2429 3.303135 TGGCCGCACGAGAAGACT 61.303 61.111 0.00 0.00 0.00 3.24
2392 2432 2.811317 CCGCACGAGAAGACTGGC 60.811 66.667 0.00 0.00 0.00 4.85
2452 2492 1.347050 CTCTCCATCTCCATCGCCAAT 59.653 52.381 0.00 0.00 0.00 3.16
2520 2564 6.219473 TCAGCTCTTCTTCTCTTACACTTTG 58.781 40.000 0.00 0.00 0.00 2.77
2521 2565 6.040955 TCAGCTCTTCTTCTCTTACACTTTGA 59.959 38.462 0.00 0.00 0.00 2.69
2522 2566 6.873076 CAGCTCTTCTTCTCTTACACTTTGAT 59.127 38.462 0.00 0.00 0.00 2.57
2528 2572 7.730364 TCTTCTCTTACACTTTGATGAAACC 57.270 36.000 0.00 0.00 0.00 3.27
2544 2588 4.079253 TGAAACCAGCCATTAGTTTCCTC 58.921 43.478 11.18 0.00 45.58 3.71
2551 2595 2.746472 GCCATTAGTTTCCTCGGCTCAT 60.746 50.000 0.00 0.00 36.58 2.90
2553 2597 4.703897 CCATTAGTTTCCTCGGCTCATTA 58.296 43.478 0.00 0.00 0.00 1.90
2693 2740 3.449227 CCGGCGTGCTACTCCAGA 61.449 66.667 6.01 0.00 0.00 3.86
2764 2823 1.198767 CGAGCGCTGAAGATCTTGAG 58.801 55.000 18.48 16.71 0.00 3.02
2830 2893 7.394359 TCCTTCTCCTTCATTTGTAATCTTTGG 59.606 37.037 0.00 0.00 0.00 3.28
2838 2901 7.353414 TCATTTGTAATCTTTGGTTTGGTCA 57.647 32.000 0.00 0.00 0.00 4.02
2854 2917 4.698201 TGGTCAGAGTGTAACATTTCCA 57.302 40.909 0.00 0.00 41.43 3.53
2867 2930 1.677576 CATTTCCACGACATCCATGGG 59.322 52.381 13.02 0.00 34.03 4.00
2884 2947 1.367840 GGGTGGCGAGGCTACTATG 59.632 63.158 4.15 0.00 39.93 2.23
2885 2948 1.400530 GGGTGGCGAGGCTACTATGT 61.401 60.000 4.15 0.00 39.93 2.29
2886 2949 0.464452 GGTGGCGAGGCTACTATGTT 59.536 55.000 4.15 0.00 39.93 2.71
2887 2950 1.684983 GGTGGCGAGGCTACTATGTTA 59.315 52.381 4.15 0.00 39.93 2.41
2888 2951 2.101917 GGTGGCGAGGCTACTATGTTAA 59.898 50.000 4.15 0.00 39.93 2.01
2889 2952 3.244112 GGTGGCGAGGCTACTATGTTAAT 60.244 47.826 4.15 0.00 39.93 1.40
2890 2953 3.741344 GTGGCGAGGCTACTATGTTAATG 59.259 47.826 0.00 0.00 37.08 1.90
2891 2954 3.639561 TGGCGAGGCTACTATGTTAATGA 59.360 43.478 0.00 0.00 0.00 2.57
2892 2955 4.238514 GGCGAGGCTACTATGTTAATGAG 58.761 47.826 0.00 0.00 0.00 2.90
2893 2956 4.262079 GGCGAGGCTACTATGTTAATGAGT 60.262 45.833 0.00 0.00 0.00 3.41
2894 2957 5.290386 GCGAGGCTACTATGTTAATGAGTT 58.710 41.667 0.00 0.00 0.00 3.01
2895 2958 5.175856 GCGAGGCTACTATGTTAATGAGTTG 59.824 44.000 0.00 0.00 0.00 3.16
2896 2959 6.504398 CGAGGCTACTATGTTAATGAGTTGA 58.496 40.000 0.00 0.00 0.00 3.18
2897 2960 6.638873 CGAGGCTACTATGTTAATGAGTTGAG 59.361 42.308 0.00 0.00 0.00 3.02
2919 2982 5.082425 AGGTTGAGGCAATCTGAATCTTTT 58.918 37.500 0.00 0.00 33.13 2.27
2920 2983 5.541484 AGGTTGAGGCAATCTGAATCTTTTT 59.459 36.000 0.00 0.00 33.13 1.94
2921 2984 5.866092 GGTTGAGGCAATCTGAATCTTTTTC 59.134 40.000 0.00 0.00 0.00 2.29
2922 2985 6.449698 GTTGAGGCAATCTGAATCTTTTTCA 58.550 36.000 0.00 0.00 0.00 2.69
2923 2986 6.845758 TGAGGCAATCTGAATCTTTTTCAT 57.154 33.333 0.00 0.00 0.00 2.57
2924 2987 7.235935 TGAGGCAATCTGAATCTTTTTCATT 57.764 32.000 0.00 0.00 0.00 2.57
2925 2988 8.352137 TGAGGCAATCTGAATCTTTTTCATTA 57.648 30.769 0.00 0.00 0.00 1.90
2926 2989 8.464404 TGAGGCAATCTGAATCTTTTTCATTAG 58.536 33.333 0.00 0.00 0.00 1.73
2940 3003 9.853177 TCTTTTTCATTAGGGAATAGATCTTCC 57.147 33.333 0.00 2.14 43.39 3.46
2945 3008 9.853177 TTCATTAGGGAATAGATCTTCCTTTTC 57.147 33.333 12.28 4.19 43.59 2.29
2953 3016 3.425659 AGATCTTCCTTTTCCCTTGCAC 58.574 45.455 0.00 0.00 0.00 4.57
2971 3034 3.711190 TGCACTACCACCTGTGATATCAT 59.289 43.478 9.02 0.00 36.38 2.45
2972 3035 4.060900 GCACTACCACCTGTGATATCATG 58.939 47.826 9.02 2.84 36.38 3.07
2992 3056 2.699321 TGAGATGAGATGCTAGCTTGCT 59.301 45.455 20.64 10.14 0.00 3.91
3131 3200 3.582120 GCCCACACCACACACACG 61.582 66.667 0.00 0.00 0.00 4.49
3132 3201 2.188207 CCCACACCACACACACGA 59.812 61.111 0.00 0.00 0.00 4.35
3138 3209 1.664649 ACCACACACACGATGCTCG 60.665 57.895 0.00 4.36 46.93 5.03
3198 3270 7.219726 GCTCGTACAGTACTTATTTAGGACAAC 59.780 40.741 9.10 0.00 40.50 3.32
3294 3373 2.224354 CCTTTTGGCATGGTCTTTGCTT 60.224 45.455 0.00 0.00 40.03 3.91
3295 3374 3.469739 CTTTTGGCATGGTCTTTGCTTT 58.530 40.909 0.00 0.00 40.03 3.51
3296 3375 2.529780 TTGGCATGGTCTTTGCTTTG 57.470 45.000 0.00 0.00 40.03 2.77
3297 3376 0.033781 TGGCATGGTCTTTGCTTTGC 59.966 50.000 0.00 0.00 40.03 3.68
3298 3377 0.319405 GGCATGGTCTTTGCTTTGCT 59.681 50.000 0.00 0.00 40.03 3.91
3537 4198 0.108709 GCGAATTGAATGGCTGGCAA 60.109 50.000 8.35 0.00 0.00 4.52
3740 4409 3.357079 GCGCTCCACAGTGGGTTG 61.357 66.667 20.14 11.16 38.32 3.77
3776 4445 2.024305 CGTAGCAGGACGCCGTAG 59.976 66.667 0.00 0.00 44.04 3.51
3777 4446 2.278661 GTAGCAGGACGCCGTAGC 60.279 66.667 0.00 0.00 44.04 3.58
3778 4447 2.752640 TAGCAGGACGCCGTAGCA 60.753 61.111 10.66 0.00 44.04 3.49
3779 4448 3.060020 TAGCAGGACGCCGTAGCAC 62.060 63.158 10.66 0.00 44.04 4.40
3781 4450 4.415332 CAGGACGCCGTAGCACGT 62.415 66.667 0.00 0.00 46.91 4.49
3787 4456 4.814294 GCCGTAGCACGTCCCCTG 62.814 72.222 7.68 0.00 40.58 4.45
3788 4457 3.066190 CCGTAGCACGTCCCCTGA 61.066 66.667 7.68 0.00 40.58 3.86
3789 4458 2.181021 CGTAGCACGTCCCCTGAC 59.819 66.667 0.00 0.00 36.74 3.51
3840 4509 3.792736 ATGGGCGCATGTACCGGT 61.793 61.111 16.43 13.98 0.00 5.28
3844 4513 2.478746 GCGCATGTACCGGTTGTG 59.521 61.111 15.04 13.70 0.00 3.33
3897 4584 2.199291 GCGTACGGCAATACTACACT 57.801 50.000 18.39 0.00 42.87 3.55
3928 4615 1.747355 CTCGAGCCCTTTCAAATGCAT 59.253 47.619 0.00 0.00 0.00 3.96
3934 4621 5.014808 AGCCCTTTCAAATGCATATCAAC 57.985 39.130 0.00 0.00 0.00 3.18
3936 4623 5.045872 GCCCTTTCAAATGCATATCAACTC 58.954 41.667 0.00 0.00 0.00 3.01
3953 4640 4.521639 TCAACTCGGAGAAACTTGCTAGTA 59.478 41.667 12.86 0.00 34.09 1.82
3960 4647 6.538021 TCGGAGAAACTTGCTAGTAGTAGTAG 59.462 42.308 0.00 7.56 33.17 2.57
3961 4648 6.315891 CGGAGAAACTTGCTAGTAGTAGTAGT 59.684 42.308 12.61 7.39 33.17 2.73
3964 4651 8.504812 AGAAACTTGCTAGTAGTAGTAGTACC 57.495 38.462 12.61 6.16 33.17 3.34
3965 4652 8.105829 AGAAACTTGCTAGTAGTAGTAGTACCA 58.894 37.037 12.61 0.00 33.17 3.25
3966 4653 7.622893 AACTTGCTAGTAGTAGTAGTACCAC 57.377 40.000 12.61 1.17 33.17 4.16
3998 4685 2.425578 GGATCGATCCGTTCTCTTCC 57.574 55.000 27.93 3.50 37.19 3.46
4002 4689 1.515954 GATCCGTTCTCTTCCGGCA 59.484 57.895 0.00 0.00 43.87 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 163 2.732094 GCGTTGTAGACACGCGGT 60.732 61.111 12.47 5.31 42.90 5.68
346 349 6.178507 CGAACATGTACTAAATTTCGCTCTG 58.821 40.000 0.00 0.00 30.62 3.35
381 384 8.978472 TGTCTCATTTACAGCCTATAAACTAGT 58.022 33.333 0.00 0.00 0.00 2.57
386 389 7.065803 GCACTTGTCTCATTTACAGCCTATAAA 59.934 37.037 0.00 0.00 0.00 1.40
387 390 6.538742 GCACTTGTCTCATTTACAGCCTATAA 59.461 38.462 0.00 0.00 0.00 0.98
390 393 4.253685 GCACTTGTCTCATTTACAGCCTA 58.746 43.478 0.00 0.00 0.00 3.93
460 463 5.423015 TCTTCAAGCCAGATGTAGATGTTC 58.577 41.667 0.00 0.00 0.00 3.18
530 533 1.680338 GTTAGGGCCTTTCGATGCAT 58.320 50.000 13.45 0.00 0.00 3.96
599 603 9.936759 AAGGTCAAAGAAAATAAGAACAACAAA 57.063 25.926 0.00 0.00 0.00 2.83
775 785 2.092592 GGATTTGGGGTTATGTCCGAGT 60.093 50.000 0.00 0.00 0.00 4.18
777 787 1.213430 GGGATTTGGGGTTATGTCCGA 59.787 52.381 0.00 0.00 0.00 4.55
784 794 4.629204 CGTTTGGATAGGGATTTGGGGTTA 60.629 45.833 0.00 0.00 0.00 2.85
785 795 3.719871 GTTTGGATAGGGATTTGGGGTT 58.280 45.455 0.00 0.00 0.00 4.11
840 850 1.705337 CCAACTCCATCGCGCGATTT 61.705 55.000 40.28 28.81 31.62 2.17
861 871 1.286248 AAGTTGGAGGGTCCGCTAAT 58.714 50.000 0.00 0.00 40.17 1.73
953 963 1.987368 GGGGGTTTTGTAGTGGGAGTA 59.013 52.381 0.00 0.00 0.00 2.59
954 964 0.775542 GGGGGTTTTGTAGTGGGAGT 59.224 55.000 0.00 0.00 0.00 3.85
955 965 3.664240 GGGGGTTTTGTAGTGGGAG 57.336 57.895 0.00 0.00 0.00 4.30
984 994 1.000993 GGGGAGCACTCTCTGAGGA 59.999 63.158 4.59 0.00 39.31 3.71
1001 1011 1.261238 GGAGAGGTGGTGAGTGGAGG 61.261 65.000 0.00 0.00 0.00 4.30
1007 1017 0.686112 GAGGAGGGAGAGGTGGTGAG 60.686 65.000 0.00 0.00 0.00 3.51
1083 1093 0.669318 TAGCTACGCTGTGGTTGTGC 60.669 55.000 0.00 0.00 40.10 4.57
1101 1111 3.632604 CACAGCAACCTAGCTAGCTACTA 59.367 47.826 20.67 2.64 44.54 1.82
1102 1112 2.428890 CACAGCAACCTAGCTAGCTACT 59.571 50.000 20.67 12.65 44.54 2.57
1103 1113 2.166664 ACACAGCAACCTAGCTAGCTAC 59.833 50.000 20.67 10.51 44.54 3.58
1416 1432 4.121317 TGGAAGCAAATCAAAGCAAACAG 58.879 39.130 0.00 0.00 0.00 3.16
1422 1438 2.919229 CGACATGGAAGCAAATCAAAGC 59.081 45.455 0.00 0.00 0.00 3.51
1465 1481 4.402474 TCCATCACGAGTCAGTATCAACAT 59.598 41.667 0.00 0.00 0.00 2.71
1579 1595 2.394563 GGAGCAGCGCCACTTCTTC 61.395 63.158 10.86 0.00 0.00 2.87
1645 1661 1.314730 TTCTTGAACGGTTCTTGCCC 58.685 50.000 20.53 0.00 0.00 5.36
1723 1739 0.471211 AGTGGACGTTGGAGGAGGAA 60.471 55.000 0.00 0.00 0.00 3.36
1804 1820 2.051614 GTCGTGTCGTGAGTCGCA 60.052 61.111 4.28 0.00 39.67 5.10
1834 1850 4.908487 TAGGGGCCGCCGTAGAGG 62.908 72.222 17.56 0.00 44.97 3.69
2061 2077 4.699522 GGTGGTCCCTGTCGGTGC 62.700 72.222 0.00 0.00 0.00 5.01
2359 2399 2.087009 CGGCCACTCGTCGAAGAAC 61.087 63.158 2.24 0.00 39.69 3.01
2389 2429 4.641645 CACGACCCCTTGCTGCCA 62.642 66.667 0.00 0.00 0.00 4.92
2392 2432 1.746615 CATCCACGACCCCTTGCTG 60.747 63.158 0.00 0.00 0.00 4.41
2452 2492 0.770166 TGGTGGTGATGGGGAGTTCA 60.770 55.000 0.00 0.00 0.00 3.18
2520 2564 4.706962 AGGAAACTAATGGCTGGTTTCATC 59.293 41.667 14.57 2.59 45.90 2.92
2521 2565 4.677182 AGGAAACTAATGGCTGGTTTCAT 58.323 39.130 14.57 7.33 45.90 2.57
2522 2566 4.079253 GAGGAAACTAATGGCTGGTTTCA 58.921 43.478 14.57 0.00 45.90 2.69
2528 2572 1.017387 GCCGAGGAAACTAATGGCTG 58.983 55.000 0.00 0.00 45.19 4.85
2544 2588 1.999735 TGAAAGCGAACTAATGAGCCG 59.000 47.619 0.00 0.00 0.00 5.52
2551 2595 2.666508 GCAGATCGTGAAAGCGAACTAA 59.333 45.455 0.00 0.00 44.38 2.24
2553 2597 1.071605 GCAGATCGTGAAAGCGAACT 58.928 50.000 0.00 0.00 44.38 3.01
2764 2823 0.749454 TCGTAGTAGGTTCCGGCCTC 60.749 60.000 3.59 0.00 39.94 4.70
2830 2893 5.298276 TGGAAATGTTACACTCTGACCAAAC 59.702 40.000 0.00 0.00 0.00 2.93
2838 2901 4.330944 TGTCGTGGAAATGTTACACTCT 57.669 40.909 2.07 0.00 33.13 3.24
2867 2930 0.464452 AACATAGTAGCCTCGCCACC 59.536 55.000 0.00 0.00 0.00 4.61
2884 2947 4.072131 TGCCTCAACCTCAACTCATTAAC 58.928 43.478 0.00 0.00 0.00 2.01
2885 2948 4.365514 TGCCTCAACCTCAACTCATTAA 57.634 40.909 0.00 0.00 0.00 1.40
2886 2949 4.365514 TTGCCTCAACCTCAACTCATTA 57.634 40.909 0.00 0.00 0.00 1.90
2887 2950 2.957402 TGCCTCAACCTCAACTCATT 57.043 45.000 0.00 0.00 0.00 2.57
2888 2951 2.957402 TTGCCTCAACCTCAACTCAT 57.043 45.000 0.00 0.00 0.00 2.90
2889 2952 2.373169 AGATTGCCTCAACCTCAACTCA 59.627 45.455 0.00 0.00 0.00 3.41
2890 2953 2.746362 CAGATTGCCTCAACCTCAACTC 59.254 50.000 0.00 0.00 0.00 3.01
2891 2954 2.373169 TCAGATTGCCTCAACCTCAACT 59.627 45.455 0.00 0.00 0.00 3.16
2892 2955 2.783135 TCAGATTGCCTCAACCTCAAC 58.217 47.619 0.00 0.00 0.00 3.18
2893 2956 3.507162 TTCAGATTGCCTCAACCTCAA 57.493 42.857 0.00 0.00 0.00 3.02
2894 2957 3.265221 AGATTCAGATTGCCTCAACCTCA 59.735 43.478 0.00 0.00 0.00 3.86
2895 2958 3.883669 AGATTCAGATTGCCTCAACCTC 58.116 45.455 0.00 0.00 0.00 3.85
2896 2959 4.313020 AAGATTCAGATTGCCTCAACCT 57.687 40.909 0.00 0.00 0.00 3.50
2897 2960 5.397142 AAAAGATTCAGATTGCCTCAACC 57.603 39.130 0.00 0.00 0.00 3.77
2936 2999 2.820197 GGTAGTGCAAGGGAAAAGGAAG 59.180 50.000 0.00 0.00 0.00 3.46
2940 3003 1.886542 GGTGGTAGTGCAAGGGAAAAG 59.113 52.381 0.00 0.00 0.00 2.27
2945 3008 0.606401 CACAGGTGGTAGTGCAAGGG 60.606 60.000 0.00 0.00 0.00 3.95
2953 3016 6.210185 TCATCTCATGATATCACAGGTGGTAG 59.790 42.308 19.79 6.65 33.59 3.18
2971 3034 2.699321 AGCAAGCTAGCATCTCATCTCA 59.301 45.455 18.83 0.00 36.85 3.27
2972 3035 3.389925 AGCAAGCTAGCATCTCATCTC 57.610 47.619 18.83 0.00 36.85 2.75
3138 3209 4.604976 CATAAAGTAAAGCTGCTGATGCC 58.395 43.478 1.35 0.00 38.71 4.40
3163 3234 1.226435 CTGTACGAGCGTCTCAGGC 60.226 63.158 15.32 0.00 31.56 4.85
3198 3270 0.865769 GACCAAGTTGGCGTACTGTG 59.134 55.000 22.25 0.00 42.67 3.66
3294 3373 0.670162 GCTTGACAGGAGCAAAGCAA 59.330 50.000 1.57 0.00 39.89 3.91
3295 3374 1.509644 CGCTTGACAGGAGCAAAGCA 61.510 55.000 7.00 0.00 40.13 3.91
3296 3375 1.208614 CGCTTGACAGGAGCAAAGC 59.791 57.895 0.35 0.00 40.13 3.51
3297 3376 1.208614 GCGCTTGACAGGAGCAAAG 59.791 57.895 8.41 0.00 40.13 2.77
3298 3377 1.509644 CTGCGCTTGACAGGAGCAAA 61.510 55.000 16.24 0.00 40.13 3.68
3740 4409 2.893398 CAGACAGCGACCTACCCC 59.107 66.667 0.00 0.00 0.00 4.95
3773 4442 2.577593 GGTCAGGGGACGTGCTAC 59.422 66.667 7.11 0.16 45.28 3.58
3774 4443 2.682494 GGGTCAGGGGACGTGCTA 60.682 66.667 7.11 0.00 45.28 3.49
3889 4558 1.589630 CTGCGGCCACAGTGTAGTA 59.410 57.895 12.88 0.00 32.78 1.82
3893 4562 4.996434 GAGCTGCGGCCACAGTGT 62.996 66.667 21.51 9.84 39.96 3.55
3913 4600 5.014808 AGTTGATATGCATTTGAAAGGGC 57.985 39.130 3.54 0.00 0.00 5.19
3928 4615 4.537135 AGCAAGTTTCTCCGAGTTGATA 57.463 40.909 0.00 0.00 30.70 2.15
3934 4621 4.705337 ACTACTAGCAAGTTTCTCCGAG 57.295 45.455 0.00 0.00 37.15 4.63
3936 4623 5.564048 ACTACTACTAGCAAGTTTCTCCG 57.436 43.478 3.85 0.00 37.15 4.63
3953 4640 7.516450 TTAACCCTAGAGTGGTACTACTACT 57.484 40.000 12.36 12.84 42.87 2.57
3960 4647 5.278858 CGATCCATTAACCCTAGAGTGGTAC 60.279 48.000 0.00 0.00 34.15 3.34
3961 4648 4.831155 CGATCCATTAACCCTAGAGTGGTA 59.169 45.833 0.00 0.00 34.15 3.25
3964 4651 5.336849 GGATCGATCCATTAACCCTAGAGTG 60.337 48.000 34.65 0.00 46.38 3.51
3965 4652 4.773149 GGATCGATCCATTAACCCTAGAGT 59.227 45.833 34.65 0.00 46.38 3.24
3966 4653 5.331876 GGATCGATCCATTAACCCTAGAG 57.668 47.826 34.65 0.00 46.38 2.43


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

AutoCloner maintained by Alex Coulton.