Multiple sequence alignment - TraesCS3A01G321400

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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 TraesCS3A01G321400 chr3A 100.000 4977 0 0 1 4977 564947489 564942513 0.000000e+00 9191
1 TraesCS3A01G321400 chr3B 93.535 4563 232 20 463 4977 552233525 552228978 0.000000e+00 6734
2 TraesCS3A01G321400 chr3B 87.602 492 33 11 1 473 552234030 552233548 3.390000e-151 545
3 TraesCS3A01G321400 chr3D 92.922 4436 213 30 571 4977 424008558 424012921 0.000000e+00 6359
4 TraesCS3A01G321400 chr3D 89.846 325 24 4 1 325 424007942 424008257 4.640000e-110 409
5 TraesCS3A01G321400 chr1D 84.112 107 11 5 1982 2087 239335121 239335020 1.140000e-16 99


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 TraesCS3A01G321400 chr3A 564942513 564947489 4976 True 9191.0 9191 100.0000 1 4977 1 chr3A.!!$R1 4976
1 TraesCS3A01G321400 chr3B 552228978 552234030 5052 True 3639.5 6734 90.5685 1 4977 2 chr3B.!!$R1 4976
2 TraesCS3A01G321400 chr3D 424007942 424012921 4979 False 3384.0 6359 91.3840 1 4977 2 chr3D.!!$F1 4976

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
733 909 0.029834 GCAATGACACCGCCATCATC 59.970 55.0 0.00 0.00 34.41 2.92 F
1152 1333 0.800631 GCAAACTACCGGTACCTTGC 59.199 55.0 27.61 27.61 33.18 4.01 F
1950 2131 0.107508 CATCACGGCATGACCCTCTT 60.108 55.0 0.00 0.00 41.24 2.85 F
2507 2703 0.397564 TCTCCACTGCAGCATTGACA 59.602 50.0 15.27 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 2001 0.244721 TGCATCACCAGAGTCAGTCG 59.755 55.000 0.00 0.0 0.00 4.18 R
2482 2678 0.761187 TGCTGCAGTGGAGAAAGAGT 59.239 50.000 16.83 0.0 0.00 3.24 R
3049 3246 0.818296 AAGCCGAGAGTTGCGATAGT 59.182 50.000 0.00 0.0 39.35 2.12 R
4310 4508 1.142870 ACCAGGTTATGCACACACACT 59.857 47.619 0.00 0.0 0.00 3.55 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
77 78 2.098117 CACCTTTCCGCCTCATCATTTC 59.902 50.000 0.00 0.00 0.00 2.17
226 234 3.076104 TCGACAGGCGAGGTACTAG 57.924 57.895 0.00 0.00 45.59 2.57
242 250 5.945191 AGGTACTAGTAATTCTATCTCCGCC 59.055 44.000 3.61 0.00 36.02 6.13
280 288 0.605319 TGTGGCTGACCCGTGATTTC 60.605 55.000 0.00 0.00 35.87 2.17
287 295 2.673368 CTGACCCGTGATTTCAGCTTAC 59.327 50.000 0.00 0.00 30.90 2.34
310 318 1.239968 GCTTCCTGGGCAGTGTCTTG 61.240 60.000 0.00 0.00 0.00 3.02
314 322 1.521450 CCTGGGCAGTGTCTTGCAAG 61.521 60.000 20.81 20.81 45.86 4.01
327 335 4.661461 GCAAGTTGCAAGGAAGCC 57.339 55.556 22.90 0.00 44.26 4.35
389 413 2.971307 TGCTTGATTCTGTACGCATCA 58.029 42.857 0.00 0.00 0.00 3.07
403 430 6.447162 TGTACGCATCATAGATTCCTAGTTG 58.553 40.000 0.00 0.00 0.00 3.16
407 443 6.258727 ACGCATCATAGATTCCTAGTTGTTTG 59.741 38.462 0.00 0.00 0.00 2.93
422 458 3.182887 TGTTTGCTATGGGGGATTTGT 57.817 42.857 0.00 0.00 0.00 2.83
435 471 0.723981 GATTTGTGAGCTGAGACGGC 59.276 55.000 0.00 0.00 35.73 5.68
468 537 2.035066 CACAGCTTTGAGGAAAAGTGGG 59.965 50.000 0.00 0.00 46.05 4.61
482 551 2.188161 GTGGGTTTCGTTGCCGGAA 61.188 57.895 5.05 0.00 33.95 4.30
494 563 1.458398 TGCCGGAATATGGTGTGTTG 58.542 50.000 5.05 0.00 0.00 3.33
498 567 2.163412 CCGGAATATGGTGTGTTGTTGG 59.837 50.000 0.00 0.00 0.00 3.77
540 609 3.873361 TCTCAACAAGTTTCAGCTCACTG 59.127 43.478 0.00 0.00 45.95 3.66
551 620 0.917533 AGCTCACTGCAGGGATCATT 59.082 50.000 21.30 2.31 45.94 2.57
552 621 1.134159 AGCTCACTGCAGGGATCATTC 60.134 52.381 21.30 6.66 45.94 2.67
639 815 2.165030 ACACTTGCTGCTATCAATTGCC 59.835 45.455 0.00 0.00 30.28 4.52
703 879 4.219725 GGCTTTATGCTTCACCAAACCTAA 59.780 41.667 0.00 0.00 42.39 2.69
711 887 6.953101 TGCTTCACCAAACCTAACTATATCA 58.047 36.000 0.00 0.00 0.00 2.15
713 889 6.260271 GCTTCACCAAACCTAACTATATCACC 59.740 42.308 0.00 0.00 0.00 4.02
724 900 3.728845 ACTATATCACCGCAATGACACC 58.271 45.455 0.00 0.00 0.00 4.16
725 901 1.581934 ATATCACCGCAATGACACCG 58.418 50.000 0.00 0.00 0.00 4.94
733 909 0.029834 GCAATGACACCGCCATCATC 59.970 55.000 0.00 0.00 34.41 2.92
740 916 2.684881 GACACCGCCATCATCATTTTCT 59.315 45.455 0.00 0.00 0.00 2.52
765 941 6.980978 TCGTTCATCTTCTCAATGATAAGACC 59.019 38.462 12.34 2.54 33.36 3.85
770 946 6.627087 TCTTCTCAATGATAAGACCAAGGT 57.373 37.500 6.94 0.00 0.00 3.50
778 954 8.966868 TCAATGATAAGACCAAGGTTTTAATCC 58.033 33.333 6.36 1.39 30.37 3.01
784 960 3.943381 GACCAAGGTTTTAATCCTACCGG 59.057 47.826 0.00 0.00 37.04 5.28
873 1050 7.339953 CGGTTAACTGTAACACTGAAGTAAAC 58.660 38.462 6.25 0.00 41.31 2.01
986 1167 1.135257 AGCGACTGTCAAGATTCGAGG 60.135 52.381 8.73 0.00 33.20 4.63
1021 1202 2.054021 TGGGAACAAGGATGACAGTCA 58.946 47.619 5.50 5.50 37.44 3.41
1068 1249 1.091771 CGGCATTGCTCGAGTGGATT 61.092 55.000 15.13 0.00 0.00 3.01
1152 1333 0.800631 GCAAACTACCGGTACCTTGC 59.199 55.000 27.61 27.61 33.18 4.01
1161 1342 1.373812 GGTACCTTGCCCGTTCTGT 59.626 57.895 4.06 0.00 0.00 3.41
1197 1378 4.225497 CTCGGCAATGAGGAACCC 57.775 61.111 0.00 0.00 32.18 4.11
1245 1426 1.539388 ACTCACAAGTCAGAGCTCTCG 59.461 52.381 14.96 9.98 35.28 4.04
1260 1441 1.001406 CTCTCGTCTTTGGCCTTCTGT 59.999 52.381 3.32 0.00 0.00 3.41
1404 1585 2.224843 TGTACTCAACGGTACTCAGGGA 60.225 50.000 0.00 0.00 41.64 4.20
1584 1765 5.243730 ACTGGACGAATCATTTGAAACCAAT 59.756 36.000 0.00 0.00 0.00 3.16
1590 1771 6.808212 ACGAATCATTTGAAACCAATGACATC 59.192 34.615 0.00 0.00 0.00 3.06
1682 1863 1.133790 GGTTCCTTGTGCTGATGATGC 59.866 52.381 0.00 0.00 0.00 3.91
1720 1901 6.114089 CCTCATGAAGCCTATGATATGGAAG 58.886 44.000 0.00 0.00 34.33 3.46
1761 1942 2.819608 TGCAGTTTTTGAGATACCAGGC 59.180 45.455 0.00 0.00 0.00 4.85
1830 2011 3.798202 AGAACAAAAAGCGACTGACTCT 58.202 40.909 0.00 0.00 0.00 3.24
1841 2022 2.548875 GACTGACTCTGGTGATGCATC 58.451 52.381 20.14 20.14 0.00 3.91
1848 2029 1.769098 CTGGTGATGCATCTTCGGCG 61.769 60.000 26.32 0.00 0.00 6.46
1853 2034 1.294659 GATGCATCTTCGGCGGATCC 61.295 60.000 19.70 0.00 0.00 3.36
1860 2041 2.238847 CTTCGGCGGATCCTGTTCCA 62.239 60.000 10.75 0.00 35.34 3.53
1869 2050 4.520492 GCGGATCCTGTTCCAAATTATGAT 59.480 41.667 10.75 0.00 35.34 2.45
1875 2056 6.359804 TCCTGTTCCAAATTATGATCCTGAG 58.640 40.000 0.00 0.00 0.00 3.35
1901 2082 2.310538 GATTAGTGGGAGCCAAATGGG 58.689 52.381 0.90 0.00 34.18 4.00
1902 2083 0.334676 TTAGTGGGAGCCAAATGGGG 59.665 55.000 0.90 0.00 34.18 4.96
1917 2098 1.690633 GGGGGCAGAGGACATCTCA 60.691 63.158 0.00 0.00 44.81 3.27
1937 2118 0.171231 TCCAGAAGACGAGCATCACG 59.829 55.000 0.00 0.00 33.17 4.35
1950 2131 0.107508 CATCACGGCATGACCCTCTT 60.108 55.000 0.00 0.00 41.24 2.85
1996 2177 8.728596 TTTAGAAGGTAAAATCCAATTTCCCA 57.271 30.769 0.00 0.00 0.00 4.37
2010 2191 5.105351 CCAATTTCCCAAACCTGGATAACTC 60.105 44.000 0.00 0.00 46.92 3.01
2050 2231 9.959749 TTTTGTTTTTATGTTGACAGATCCTAC 57.040 29.630 0.00 0.00 0.00 3.18
2080 2261 2.035066 GGATAATTGTGCAGATGCCACC 59.965 50.000 1.72 0.00 41.18 4.61
2105 2286 2.302445 CCCCAAATTCCAGTTGCATCAA 59.698 45.455 0.00 0.00 0.00 2.57
2145 2326 8.868522 AAGATTCTTGGTGAAACTGAATCATA 57.131 30.769 13.93 0.00 43.28 2.15
2147 2328 8.900781 AGATTCTTGGTGAAACTGAATCATATG 58.099 33.333 13.93 0.00 43.28 1.78
2151 2332 8.270030 TCTTGGTGAAACTGAATCATATGAGAT 58.730 33.333 11.78 2.47 36.74 2.75
2155 2336 7.496920 GGTGAAACTGAATCATATGAGATGACA 59.503 37.037 11.78 5.89 36.74 3.58
2157 2338 9.106070 TGAAACTGAATCATATGAGATGACAAG 57.894 33.333 11.78 4.58 0.00 3.16
2170 2351 4.586884 AGATGACAAGTGACAGCATCATT 58.413 39.130 0.00 0.00 40.28 2.57
2331 2512 9.571810 TCATGACACAGCAAATAATTGTTAATC 57.428 29.630 0.00 0.00 38.85 1.75
2470 2666 5.239306 TCACTATGTTGCTTCAGAAGGTTTG 59.761 40.000 12.30 0.00 0.00 2.93
2474 2670 5.906113 TGTTGCTTCAGAAGGTTTGTTAA 57.094 34.783 12.30 0.00 0.00 2.01
2482 2678 7.491048 GCTTCAGAAGGTTTGTTAATTTTGTCA 59.509 33.333 12.30 0.00 0.00 3.58
2497 2693 2.533266 TGTCACTCTTTCTCCACTGC 57.467 50.000 0.00 0.00 0.00 4.40
2504 2700 2.156917 TCTTTCTCCACTGCAGCATTG 58.843 47.619 15.27 5.76 0.00 2.82
2507 2703 0.397564 TCTCCACTGCAGCATTGACA 59.602 50.000 15.27 0.00 0.00 3.58
2547 2743 4.717280 ACCTCGGGATTCATTTCTACTCTT 59.283 41.667 0.00 0.00 0.00 2.85
2633 2829 9.780413 GCTGAAGTTGAAGATAATCCTAAAAAG 57.220 33.333 0.00 0.00 0.00 2.27
2636 2832 7.646548 AGTTGAAGATAATCCTAAAAAGGCC 57.353 36.000 0.00 0.00 0.00 5.19
2641 2837 7.228706 TGAAGATAATCCTAAAAAGGCCGAATC 59.771 37.037 0.00 0.00 0.00 2.52
2644 2840 3.553828 TCCTAAAAAGGCCGAATCGAT 57.446 42.857 3.36 0.00 0.00 3.59
2645 2841 3.463944 TCCTAAAAAGGCCGAATCGATC 58.536 45.455 3.36 0.00 0.00 3.69
2669 2865 5.014858 GGTGATACGGGAATAGATGGACTA 58.985 45.833 0.00 0.00 35.42 2.59
2694 2890 4.277515 TCACAAGATCCTTCCAGTTCAG 57.722 45.455 0.00 0.00 0.00 3.02
2698 2894 4.077822 CAAGATCCTTCCAGTTCAGCTTT 58.922 43.478 0.00 0.00 0.00 3.51
2709 2905 4.986659 CCAGTTCAGCTTTCAAAGATTTGG 59.013 41.667 0.00 0.00 38.66 3.28
2712 2908 7.373493 CAGTTCAGCTTTCAAAGATTTGGTAT 58.627 34.615 0.00 0.00 38.66 2.73
2726 2922 8.661352 AAGATTTGGTATCAAAAGGTTTGTTG 57.339 30.769 5.02 0.00 44.83 3.33
2727 2923 8.017418 AGATTTGGTATCAAAAGGTTTGTTGA 57.983 30.769 5.02 0.00 44.83 3.18
2731 2927 9.454859 TTTGGTATCAAAAGGTTTGTTGATTTT 57.545 25.926 0.00 0.00 40.71 1.82
2757 2953 4.142315 CCTTCCATCCAGCACAGTATTTTG 60.142 45.833 0.00 0.00 0.00 2.44
2771 2967 7.305474 CACAGTATTTTGAATGTGGTCCTTAC 58.695 38.462 0.00 0.00 39.45 2.34
2787 2984 8.311109 GTGGTCCTTACATTTAACCATTTGATT 58.689 33.333 0.00 0.00 41.71 2.57
2801 2998 4.201950 CCATTTGATTAGGTGCGAAAGAGG 60.202 45.833 0.00 0.00 0.00 3.69
2860 3057 2.435805 GGTATCTCAGGGTCTTGATGCA 59.564 50.000 0.00 0.00 0.00 3.96
2920 3117 3.107402 AGGAGACCATCTCTTAGCACA 57.893 47.619 5.84 0.00 42.95 4.57
2959 3156 2.102578 GCCTACAATCTTGCCATTGGT 58.897 47.619 4.26 0.00 37.98 3.67
2992 3189 0.774096 TCCCATCCCCAACCTTGACA 60.774 55.000 0.00 0.00 0.00 3.58
3038 3235 5.128827 TCTTCGGCTAGTGTAAATGGAGAAT 59.871 40.000 0.00 0.00 0.00 2.40
3049 3246 7.125811 AGTGTAAATGGAGAATTGAGGCTACTA 59.874 37.037 0.00 0.00 0.00 1.82
3055 3252 5.473846 TGGAGAATTGAGGCTACTACTATCG 59.526 44.000 0.00 0.00 0.00 2.92
3137 3334 1.005037 TATGGGCGTGGCGATGATC 60.005 57.895 1.20 0.00 0.00 2.92
3190 3387 2.095053 GCTCGAGAGAAATGTTTCTGGC 59.905 50.000 18.75 4.02 46.84 4.85
3249 3446 1.893786 GTGAGAGCACCATCGACCT 59.106 57.895 0.00 0.00 39.14 3.85
3310 3507 2.733669 CCTCTGCAGGGAGCTGGAG 61.734 68.421 17.43 1.25 45.94 3.86
3328 3525 1.209019 GAGGAAGAGAGGAATGCTGCA 59.791 52.381 4.13 4.13 0.00 4.41
3606 3803 5.009010 CCTTTGAAGAACAACATAGCACTGT 59.991 40.000 0.00 0.00 38.29 3.55
3667 3864 4.137543 GTTTGAGGAAGCTGGAGAAGAAA 58.862 43.478 0.00 0.00 0.00 2.52
3697 3894 7.011950 CACTTGTACTCCAACAACAATACTTCA 59.988 37.037 0.00 0.00 35.56 3.02
3907 4104 6.183361 ACTCCCTTAAGAATGGAAAAGAAGGT 60.183 38.462 3.36 0.00 31.85 3.50
3997 4194 8.752005 AATAGCATTGTGGATTTTAGCTCTTA 57.248 30.769 0.00 0.00 32.49 2.10
4120 4317 6.515832 AGGAACTTTGTTTTTGGCTATTGAG 58.484 36.000 0.00 0.00 27.25 3.02
4133 4330 4.141251 TGGCTATTGAGGGGAGATTTTACC 60.141 45.833 0.00 0.00 0.00 2.85
4164 4361 4.080582 ACTTGGCAAGTATACTGGCATGTA 60.081 41.667 30.31 12.62 44.72 2.29
4233 4431 5.173664 GGACATAGTAGTGGGTAACAACAC 58.826 45.833 0.00 0.00 37.86 3.32
4260 4458 6.601613 CCAAGTGGCCTACTGATTTTGTTATA 59.398 38.462 3.32 0.00 40.26 0.98
4310 4508 1.277842 AGGAAGTGTGTGTGTGTGTGA 59.722 47.619 0.00 0.00 0.00 3.58
4321 4519 0.321122 TGTGTGTGAGTGTGTGTGCA 60.321 50.000 0.00 0.00 0.00 4.57
4394 4598 1.701292 CCATGATCCTGGCATCCTACA 59.299 52.381 3.90 0.00 0.00 2.74
4596 4800 6.959361 AGACTAAACTGCAACACTTTACATG 58.041 36.000 0.00 0.00 0.00 3.21
4669 4885 0.883833 CCTTGAACCTGCACCATGTC 59.116 55.000 0.00 0.00 0.00 3.06
4672 4888 2.034066 AACCTGCACCATGTCCGG 59.966 61.111 0.00 0.00 0.00 5.14
4673 4889 2.748058 GAACCTGCACCATGTCCGGT 62.748 60.000 0.00 0.00 41.07 5.28
4674 4890 2.034066 CCTGCACCATGTCCGGTT 59.966 61.111 0.00 0.00 37.07 4.44
4675 4891 1.298340 CCTGCACCATGTCCGGTTA 59.702 57.895 0.00 0.00 37.07 2.85
4676 4892 1.024579 CCTGCACCATGTCCGGTTAC 61.025 60.000 0.00 0.00 37.07 2.50
4677 4893 0.321210 CTGCACCATGTCCGGTTACA 60.321 55.000 0.00 0.00 37.07 2.41
4678 4894 0.108774 TGCACCATGTCCGGTTACAA 59.891 50.000 0.00 0.00 37.07 2.41
4793 5009 3.019564 GCTCTCCCACTTGCATAATTGT 58.980 45.455 0.00 0.00 0.00 2.71
4825 5041 1.082104 CTGCTGCGAAAACCCGTTC 60.082 57.895 0.00 0.00 0.00 3.95
4836 5052 0.324943 AACCCGTTCACTCCAGGATG 59.675 55.000 0.00 0.00 0.00 3.51
4902 5118 0.394352 GAGTCCGCCATTCCATTGGT 60.394 55.000 1.86 0.00 39.11 3.67
4939 5155 0.786435 AAAATTGCCCCTCTCCCAGT 59.214 50.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.686816 CCGCCGAAACGAGCCAAAT 61.687 57.895 0.00 0.00 34.06 2.32
34 35 4.003648 GGCAGGGAAATATATTCTCCACG 58.996 47.826 19.57 13.88 0.00 4.94
36 37 4.202567 GGTGGCAGGGAAATATATTCTCCA 60.203 45.833 19.57 11.19 0.00 3.86
77 78 2.132996 AGCATCAGGAGGAGGAGCG 61.133 63.158 0.00 0.00 0.00 5.03
222 230 4.087907 GGGGCGGAGATAGAATTACTAGT 58.912 47.826 0.00 0.00 34.35 2.57
226 234 1.672145 GCGGGGCGGAGATAGAATTAC 60.672 57.143 0.00 0.00 0.00 1.89
242 250 1.068333 CAGAACAAAATCACAGGCGGG 60.068 52.381 0.00 0.00 0.00 6.13
280 288 1.815003 CCCAGGAAGCAAAGTAAGCTG 59.185 52.381 0.00 0.00 42.53 4.24
287 295 0.825010 ACACTGCCCAGGAAGCAAAG 60.825 55.000 0.00 0.00 40.35 2.77
310 318 0.319297 CAGGCTTCCTTGCAACTTGC 60.319 55.000 6.82 6.82 45.29 4.01
314 322 0.746659 ACAACAGGCTTCCTTGCAAC 59.253 50.000 0.00 0.00 34.04 4.17
339 361 6.706746 GCCACGAGCTTAAAACTAAGAATAG 58.293 40.000 0.00 0.00 38.99 1.73
389 413 7.227156 CCCATAGCAAACAACTAGGAATCTAT 58.773 38.462 0.00 0.00 0.00 1.98
403 430 3.096092 TCACAAATCCCCCATAGCAAAC 58.904 45.455 0.00 0.00 0.00 2.93
407 443 1.133668 AGCTCACAAATCCCCCATAGC 60.134 52.381 0.00 0.00 0.00 2.97
422 458 1.260538 AATCCTGCCGTCTCAGCTCA 61.261 55.000 0.00 0.00 32.87 4.26
435 471 1.915141 AAGCTGTGGGTGAAATCCTG 58.085 50.000 0.00 0.00 0.00 3.86
482 551 1.173043 CCGCCAACAACACACCATAT 58.827 50.000 0.00 0.00 0.00 1.78
494 563 1.197036 GAGCAACTAAAGTCCGCCAAC 59.803 52.381 0.00 0.00 0.00 3.77
498 567 0.444260 GCTGAGCAACTAAAGTCCGC 59.556 55.000 0.00 0.00 0.00 5.54
540 609 2.997899 CAGGACGAATGATCCCTGC 58.002 57.895 0.00 0.00 39.59 4.85
639 815 0.527565 CCGAATGCCAGGTTGGAAAG 59.472 55.000 0.00 0.00 40.96 2.62
703 879 3.728845 GGTGTCATTGCGGTGATATAGT 58.271 45.455 0.00 0.00 0.00 2.12
711 887 3.918253 ATGGCGGTGTCATTGCGGT 62.918 57.895 0.00 0.00 0.00 5.68
713 889 1.717791 ATGATGGCGGTGTCATTGCG 61.718 55.000 0.00 0.00 31.26 4.85
724 900 3.063861 TGAACGAGAAAATGATGATGGCG 59.936 43.478 0.00 0.00 0.00 5.69
725 901 4.621068 TGAACGAGAAAATGATGATGGC 57.379 40.909 0.00 0.00 0.00 4.40
733 909 7.745972 TCATTGAGAAGATGAACGAGAAAATG 58.254 34.615 0.00 0.00 30.96 2.32
740 916 6.980978 GGTCTTATCATTGAGAAGATGAACGA 59.019 38.462 22.61 0.86 41.03 3.85
778 954 4.457603 CCTAGAGACATCAGAATCCGGTAG 59.542 50.000 0.00 0.00 0.00 3.18
784 960 6.322712 ACCTGTAACCTAGAGACATCAGAATC 59.677 42.308 0.00 0.00 0.00 2.52
851 1027 9.090692 GTGAGTTTACTTCAGTGTTACAGTTAA 57.909 33.333 0.00 0.00 0.00 2.01
873 1050 9.121517 CAAAGTTAATAATCAGCAAAGTGTGAG 57.878 33.333 0.00 0.00 0.00 3.51
996 1177 3.156293 TGTCATCCTTGTTCCCATTGTG 58.844 45.455 0.00 0.00 0.00 3.33
1041 1222 2.437359 AGCAATGCCGAGGACAGC 60.437 61.111 0.00 0.00 0.00 4.40
1068 1249 5.007039 GTCGATGAATAGCAGAAGCATCAAA 59.993 40.000 0.00 0.00 45.49 2.69
1152 1333 1.275291 TCTAGCCTTGAACAGAACGGG 59.725 52.381 0.00 0.00 0.00 5.28
1161 1342 3.068732 CGAGGACATGATCTAGCCTTGAA 59.931 47.826 0.00 0.00 32.88 2.69
1197 1378 4.815308 CAGATCAATTCCCTGTAGAAGCAG 59.185 45.833 0.00 0.00 36.31 4.24
1245 1426 1.869690 GCGACAGAAGGCCAAAGAC 59.130 57.895 5.01 0.00 0.00 3.01
1260 1441 0.250295 CAAGTTTCTGGTGGAGGCGA 60.250 55.000 0.00 0.00 0.00 5.54
1404 1585 4.565652 GGAGAATGTAACACACCATCACCT 60.566 45.833 0.00 0.00 0.00 4.00
1512 1693 6.030228 GCAAATCTTTGGTGACTTAGCATAC 58.970 40.000 4.93 0.00 38.57 2.39
1584 1765 3.169512 TCACTCTGGTGGTAGATGTCA 57.830 47.619 0.00 0.00 43.17 3.58
1590 1771 5.538053 AGATGTATGATCACTCTGGTGGTAG 59.462 44.000 0.00 0.00 43.17 3.18
1682 1863 3.036819 TCATGAGGGTGAGAATCTCTGG 58.963 50.000 11.92 0.00 34.92 3.86
1720 1901 4.081752 TGCATCTTCCTGAAAGTCTCTCTC 60.082 45.833 0.00 0.00 36.31 3.20
1761 1942 3.148084 ACCTCAGGGTGTGGAACG 58.852 61.111 0.00 0.00 45.43 3.95
1820 2001 0.244721 TGCATCACCAGAGTCAGTCG 59.755 55.000 0.00 0.00 0.00 4.18
1830 2011 1.815003 CGCCGAAGATGCATCACCA 60.815 57.895 27.81 0.00 0.00 4.17
1841 2022 1.521681 GGAACAGGATCCGCCGAAG 60.522 63.158 5.98 0.00 43.43 3.79
1848 2029 6.208204 CAGGATCATAATTTGGAACAGGATCC 59.792 42.308 2.48 2.48 46.23 3.36
1853 2034 7.012138 CACTCTCAGGATCATAATTTGGAACAG 59.988 40.741 0.00 0.00 42.39 3.16
1860 2041 9.775854 CTAATCACACTCTCAGGATCATAATTT 57.224 33.333 0.00 0.00 0.00 1.82
1869 2050 3.099905 CCCACTAATCACACTCTCAGGA 58.900 50.000 0.00 0.00 0.00 3.86
1875 2056 1.555075 TGGCTCCCACTAATCACACTC 59.445 52.381 0.00 0.00 0.00 3.51
1901 2082 0.396060 GGATGAGATGTCCTCTGCCC 59.604 60.000 0.00 0.00 42.44 5.36
1902 2083 1.070445 CTGGATGAGATGTCCTCTGCC 59.930 57.143 0.00 0.00 42.44 4.85
1917 2098 1.202348 CGTGATGCTCGTCTTCTGGAT 60.202 52.381 0.00 0.00 0.00 3.41
1937 2118 1.322442 GGCAATAAGAGGGTCATGCC 58.678 55.000 0.00 0.00 45.54 4.40
1987 2168 5.105351 GGAGTTATCCAGGTTTGGGAAATTG 60.105 44.000 0.00 0.00 45.87 2.32
1988 2169 5.023452 GGAGTTATCCAGGTTTGGGAAATT 58.977 41.667 0.00 0.00 45.87 1.82
1990 2171 4.042271 GGAGTTATCCAGGTTTGGGAAA 57.958 45.455 0.00 0.00 45.87 3.13
2010 2191 8.987890 CATAAAAACAAAAGTGGAAATAGTGGG 58.012 33.333 0.00 0.00 0.00 4.61
2050 2231 5.353111 TCTGCACAATTATCCATGCAATTG 58.647 37.500 17.32 17.32 46.75 2.32
2080 2261 1.336795 GCAACTGGAATTTGGGGAACG 60.337 52.381 0.00 0.00 0.00 3.95
2126 2307 7.854557 TCTCATATGATTCAGTTTCACCAAG 57.145 36.000 5.72 0.00 0.00 3.61
2145 2326 3.690475 TGCTGTCACTTGTCATCTCAT 57.310 42.857 0.00 0.00 0.00 2.90
2147 2328 3.593096 TGATGCTGTCACTTGTCATCTC 58.407 45.455 0.00 0.00 35.74 2.75
2151 2332 3.742385 TCAATGATGCTGTCACTTGTCA 58.258 40.909 0.00 0.00 40.28 3.58
2155 2336 3.959293 TGGATCAATGATGCTGTCACTT 58.041 40.909 15.51 0.00 40.28 3.16
2157 2338 6.652062 TGTATATGGATCAATGATGCTGTCAC 59.348 38.462 15.51 9.04 40.28 3.67
2191 2372 5.577164 AGCATAGTGTTGTTCGAGTATTGTC 59.423 40.000 0.00 0.00 0.00 3.18
2331 2512 2.158928 CCCTGAGCTTCTTCTGGATCAG 60.159 54.545 0.00 0.00 43.12 2.90
2470 2666 7.857885 CAGTGGAGAAAGAGTGACAAAATTAAC 59.142 37.037 0.00 0.00 0.00 2.01
2474 2670 4.276926 GCAGTGGAGAAAGAGTGACAAAAT 59.723 41.667 0.00 0.00 0.00 1.82
2482 2678 0.761187 TGCTGCAGTGGAGAAAGAGT 59.239 50.000 16.83 0.00 0.00 3.24
2497 2693 9.702494 TCAGTTAAGATAGATATGTCAATGCTG 57.298 33.333 0.00 0.00 0.00 4.41
2504 2700 8.024285 CCGAGGTTCAGTTAAGATAGATATGTC 58.976 40.741 0.00 0.00 0.00 3.06
2507 2703 7.239438 TCCCGAGGTTCAGTTAAGATAGATAT 58.761 38.462 0.00 0.00 0.00 1.63
2525 2721 4.946478 AGAGTAGAAATGAATCCCGAGG 57.054 45.455 0.00 0.00 0.00 4.63
2641 2837 2.745821 TCTATTCCCGTATCACCGATCG 59.254 50.000 8.51 8.51 0.00 3.69
2644 2840 2.823747 CCATCTATTCCCGTATCACCGA 59.176 50.000 0.00 0.00 0.00 4.69
2645 2841 2.823747 TCCATCTATTCCCGTATCACCG 59.176 50.000 0.00 0.00 0.00 4.94
2654 2850 6.174720 TGTGATGTTAGTCCATCTATTCCC 57.825 41.667 0.00 0.00 41.47 3.97
2669 2865 4.647564 ACTGGAAGGATCTTGTGATGTT 57.352 40.909 0.00 0.00 39.30 2.71
2678 2874 3.328931 TGAAAGCTGAACTGGAAGGATCT 59.671 43.478 0.00 0.00 39.30 2.75
2694 2890 7.657354 ACCTTTTGATACCAAATCTTTGAAAGC 59.343 33.333 0.00 0.00 41.43 3.51
2698 2894 8.482128 ACAAACCTTTTGATACCAAATCTTTGA 58.518 29.630 11.41 0.00 41.43 2.69
2712 2908 9.157104 GAAGGTAAAAATCAACAAACCTTTTGA 57.843 29.630 5.67 0.00 45.04 2.69
2726 2922 4.462483 TGTGCTGGATGGAAGGTAAAAATC 59.538 41.667 0.00 0.00 0.00 2.17
2727 2923 4.415596 TGTGCTGGATGGAAGGTAAAAAT 58.584 39.130 0.00 0.00 0.00 1.82
2731 2927 1.985159 ACTGTGCTGGATGGAAGGTAA 59.015 47.619 0.00 0.00 0.00 2.85
2757 2953 6.827586 TGGTTAAATGTAAGGACCACATTC 57.172 37.500 9.89 0.71 43.94 2.67
2771 2967 6.559810 TCGCACCTAATCAAATGGTTAAATG 58.440 36.000 0.00 0.00 30.72 2.32
2787 2984 1.195115 ATGAGCCTCTTTCGCACCTA 58.805 50.000 0.00 0.00 0.00 3.08
2790 2987 2.545946 GGAATATGAGCCTCTTTCGCAC 59.454 50.000 0.00 0.00 0.00 5.34
2801 2998 2.357009 CAGCAACTGGTGGAATATGAGC 59.643 50.000 0.86 0.00 39.67 4.26
2920 3117 2.939103 GGCTTCGTTCATGCTAATCTGT 59.061 45.455 0.00 0.00 0.00 3.41
2992 3189 3.011032 AGCCCTTTCCAAGAATCACATCT 59.989 43.478 0.00 0.00 0.00 2.90
3038 3235 3.952323 AGTTGCGATAGTAGTAGCCTCAA 59.048 43.478 0.00 0.00 39.35 3.02
3049 3246 0.818296 AAGCCGAGAGTTGCGATAGT 59.182 50.000 0.00 0.00 39.35 2.12
3055 3252 1.743252 CCTGGAAGCCGAGAGTTGC 60.743 63.158 0.00 0.00 0.00 4.17
3130 3327 4.614946 TGTTCTGCACTATCAGATCATCG 58.385 43.478 0.00 0.00 42.12 3.84
3137 3334 7.547019 TCTTCTTGTTATGTTCTGCACTATCAG 59.453 37.037 0.00 0.00 35.46 2.90
3190 3387 2.202932 CCGTCCAGCGATTCCAGG 60.203 66.667 0.00 0.00 44.77 4.45
3249 3446 2.757314 AGATCAATCTGTCGTCTCAGCA 59.243 45.455 0.00 0.00 35.42 4.41
3310 3507 1.666054 CTGCAGCATTCCTCTCTTCC 58.334 55.000 0.00 0.00 0.00 3.46
3543 3740 2.034687 CTGTTGGCCCTCCACCTG 59.965 66.667 0.00 0.00 43.33 4.00
3606 3803 4.511527 CCTCTCATCTTCAAGCAAAGCTA 58.488 43.478 0.00 0.00 38.25 3.32
3667 3864 4.839121 TGTTGTTGGAGTACAAGTGAAGT 58.161 39.130 0.00 0.00 40.38 3.01
3907 4104 4.431809 CAATTTCCCTTATGAATTGCGCA 58.568 39.130 5.66 5.66 34.98 6.09
3997 4194 2.088423 TGCACGAAGAGGTTTTGTGTT 58.912 42.857 8.57 0.00 33.23 3.32
4120 4317 5.084519 AGTTCTTTTGGGTAAAATCTCCCC 58.915 41.667 0.00 0.00 42.80 4.81
4164 4361 8.026607 TCGTCTCACAAAGAAAAGAAAACAAAT 58.973 29.630 0.00 0.00 35.21 2.32
4233 4431 2.496899 AATCAGTAGGCCACTTGGTG 57.503 50.000 5.01 0.00 34.26 4.17
4260 4458 6.777580 AGTCCCAAATACTGATCACTTGTTTT 59.222 34.615 0.00 0.00 0.00 2.43
4277 4475 2.241176 ACACTTCCTGTTCAGTCCCAAA 59.759 45.455 0.00 0.00 0.00 3.28
4310 4508 1.142870 ACCAGGTTATGCACACACACT 59.857 47.619 0.00 0.00 0.00 3.55
4321 4519 4.348168 AGTCACAAGTCTCAACCAGGTTAT 59.652 41.667 3.89 0.00 0.00 1.89
4655 4871 2.034066 CCGGACATGGTGCAGGTT 59.966 61.111 0.00 0.00 0.00 3.50
4678 4894 5.530915 TGAATGCTGCTTGTAAGTTGTAACT 59.469 36.000 0.00 0.00 42.04 2.24
4793 5009 0.911769 CAGCAGATGGGGGACTACAA 59.088 55.000 0.00 0.00 0.00 2.41
4825 5041 1.100510 CAATGGTGCATCCTGGAGTG 58.899 55.000 1.52 2.33 37.07 3.51
4836 5052 4.026356 AGCTATCCTAATCCAATGGTGC 57.974 45.455 0.00 0.00 0.00 5.01
4902 5118 6.638610 CAATTTTCCACATTGGGTGCTTATA 58.361 36.000 0.00 0.00 46.50 0.98
4939 5155 2.093816 CAGGCTGAATGCTCTACACAGA 60.094 50.000 9.42 0.00 42.39 3.41


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

AutoCloner maintained by Alex Coulton.