Multiple sequence alignment - TraesCS2D01G501800

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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 TraesCS2D01G501800 chr2D 100.000 2970 0 0 1 2970 596028536 596031505 0.000000e+00 5485.0
1 TraesCS2D01G501800 chr2B 88.204 2221 134 44 1 2193 724409338 724411458 0.000000e+00 2532.0
2 TraesCS2D01G501800 chr2A 89.642 1902 109 37 698 2545 729687750 729689617 0.000000e+00 2340.0
3 TraesCS2D01G501800 chr2A 92.250 400 17 4 2543 2938 729691565 729691954 3.340000e-154 555.0
4 TraesCS2D01G501800 chr2A 84.817 382 30 14 1 366 729687131 729687500 2.810000e-95 359.0
5 TraesCS2D01G501800 chr2A 88.053 226 18 4 397 619 729687502 729687721 2.940000e-65 259.0
6 TraesCS2D01G501800 chr7D 85.714 77 10 1 2474 2549 10560605 10560681 2.450000e-11 80.5
7 TraesCS2D01G501800 chr5D 83.117 77 9 3 1028 1102 271900001 271900075 1.910000e-07 67.6
8 TraesCS2D01G501800 chr5B 83.117 77 9 3 1028 1102 308110203 308110277 1.910000e-07 67.6
9 TraesCS2D01G501800 chr5A 83.117 77 9 3 1028 1102 361709268 361709342 1.910000e-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 TraesCS2D01G501800 chr2D 596028536 596031505 2969 False 5485.00 5485 100.0000 1 2970 1 chr2D.!!$F1 2969
1 TraesCS2D01G501800 chr2B 724409338 724411458 2120 False 2532.00 2532 88.2040 1 2193 1 chr2B.!!$F1 2192
2 TraesCS2D01G501800 chr2A 729687131 729691954 4823 False 878.25 2340 88.6905 1 2938 4 chr2A.!!$F1 2937

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
239 248 0.611062 TGGGTCAAGACGGACTCGAT 60.611 55.000 0.00 0.00 41.3 3.59 F
585 613 1.012841 CAAATCTGGCCTCGAGAAGC 58.987 55.000 15.71 9.76 0.0 3.86 F
625 656 1.076677 TCGGGAGTAGTTGAAGGGAGT 59.923 52.381 0.00 0.00 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 1860 0.312102 GCACCAGCTTCTTGACAACC 59.688 55.0 0.00 0.00 37.91 3.77 R
1828 1902 0.533032 GGTATATGGCGCTCTCCTCC 59.467 60.0 7.64 0.04 0.00 4.30 R
2614 4649 0.179094 GCCGTACCCATCGATCACAA 60.179 55.0 0.00 0.00 0.00 3.33 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
18 19 3.035727 GGAGGAGAGCCGATCGAC 58.964 66.667 18.66 4.51 39.96 4.20
34 35 3.116079 TCGACTTGGTTTCTACCCAAC 57.884 47.619 0.00 0.00 44.35 3.77
80 81 9.474920 CAGCCAAAGTTACTTTTCATTATTTCA 57.525 29.630 7.71 0.00 30.60 2.69
114 115 5.598769 AGCGATTTATTACTCCACACTACC 58.401 41.667 0.00 0.00 0.00 3.18
127 128 7.180663 ACTCCACACTACCACTAGTATACTTT 58.819 38.462 11.40 0.00 31.46 2.66
144 145 8.880750 AGTATACTTTTCCTTAAAGCTAAAGCG 58.119 33.333 0.00 0.00 45.87 4.68
188 197 5.108027 GCACAACATAACATTCAAACCGAAC 60.108 40.000 0.00 0.00 36.12 3.95
219 228 2.394563 GCTTCAACGGCTCTGCTCC 61.395 63.158 0.00 0.00 0.00 4.70
220 229 1.294780 CTTCAACGGCTCTGCTCCT 59.705 57.895 0.00 0.00 0.00 3.69
221 230 1.004560 TTCAACGGCTCTGCTCCTG 60.005 57.895 0.00 0.00 0.00 3.86
229 238 1.548357 GCTCTGCTCCTGGGTCAAGA 61.548 60.000 0.00 0.00 0.00 3.02
239 248 0.611062 TGGGTCAAGACGGACTCGAT 60.611 55.000 0.00 0.00 41.30 3.59
403 428 2.494870 GCCCATTGACAGCTCAGAAAAT 59.505 45.455 0.00 0.00 0.00 1.82
404 429 3.675228 GCCCATTGACAGCTCAGAAAATG 60.675 47.826 0.00 0.00 0.00 2.32
405 430 3.508762 CCATTGACAGCTCAGAAAATGC 58.491 45.455 0.00 0.00 0.00 3.56
406 431 3.192844 CCATTGACAGCTCAGAAAATGCT 59.807 43.478 0.00 0.00 37.56 3.79
407 432 4.397103 CCATTGACAGCTCAGAAAATGCTA 59.603 41.667 0.00 0.00 35.05 3.49
443 468 3.905678 CGCTCGCTCCCGGAAGAT 61.906 66.667 0.73 0.00 34.56 2.40
444 469 2.501610 GCTCGCTCCCGGAAGATT 59.498 61.111 0.73 0.00 34.56 2.40
471 496 5.732633 TGATTGATTGGTGGCCATTTTTAG 58.267 37.500 9.72 0.00 31.53 1.85
475 500 4.020662 TGATTGGTGGCCATTTTTAGTTCC 60.021 41.667 9.72 1.73 31.53 3.62
492 520 4.003648 AGTTCCTGATGACAAATTCGACC 58.996 43.478 0.00 0.00 0.00 4.79
523 551 6.815641 CACACTCTACTTTGCATCTTGATAGT 59.184 38.462 0.00 0.00 0.00 2.12
534 562 7.745620 TGCATCTTGATAGTATCGTTCTAGA 57.254 36.000 5.68 0.00 0.00 2.43
585 613 1.012841 CAAATCTGGCCTCGAGAAGC 58.987 55.000 15.71 9.76 0.00 3.86
613 641 2.635915 ACCAACTGTGAATTCGGGAGTA 59.364 45.455 0.04 0.00 0.00 2.59
619 650 4.039973 ACTGTGAATTCGGGAGTAGTTGAA 59.960 41.667 0.04 0.00 0.00 2.69
624 655 1.848652 TCGGGAGTAGTTGAAGGGAG 58.151 55.000 0.00 0.00 0.00 4.30
625 656 1.076677 TCGGGAGTAGTTGAAGGGAGT 59.923 52.381 0.00 0.00 0.00 3.85
627 658 2.426381 CGGGAGTAGTTGAAGGGAGTAC 59.574 54.545 0.00 0.00 0.00 2.73
628 659 3.710724 GGGAGTAGTTGAAGGGAGTACT 58.289 50.000 0.00 0.00 36.29 2.73
630 661 4.531339 GGGAGTAGTTGAAGGGAGTACTTT 59.469 45.833 0.00 0.00 34.31 2.66
631 662 5.012871 GGGAGTAGTTGAAGGGAGTACTTTT 59.987 44.000 0.00 0.00 34.31 2.27
632 663 6.465464 GGGAGTAGTTGAAGGGAGTACTTTTT 60.465 42.308 0.00 0.00 34.31 1.94
680 711 3.439540 CGCCCCCAACGGAATGTG 61.440 66.667 0.00 0.00 0.00 3.21
739 770 7.514747 CGGCAAGATAAAAAGCGTTACTAGTAG 60.515 40.741 2.23 0.00 0.00 2.57
743 774 9.513727 AAGATAAAAAGCGTTACTAGTAGTAGC 57.486 33.333 12.78 12.78 31.47 3.58
836 873 3.468140 GCTCACCCGGGGGAGTAC 61.468 72.222 45.05 30.41 38.96 2.73
911 953 4.416738 GTCCCCTGCCTGCCACTC 62.417 72.222 0.00 0.00 0.00 3.51
912 954 4.980592 TCCCCTGCCTGCCACTCA 62.981 66.667 0.00 0.00 0.00 3.41
914 956 2.674380 CCCTGCCTGCCACTCAAC 60.674 66.667 0.00 0.00 0.00 3.18
915 957 2.433446 CCTGCCTGCCACTCAACT 59.567 61.111 0.00 0.00 0.00 3.16
1166 1220 2.125350 CCCCTTCTCTCGCTGTGC 60.125 66.667 0.00 0.00 0.00 4.57
1187 1246 3.740128 ATGCACCGTCGATCTGCCC 62.740 63.158 8.83 0.00 0.00 5.36
1279 1338 5.068460 AGTGTTCTCCTCCTGATTATTCTCG 59.932 44.000 0.00 0.00 0.00 4.04
1280 1339 4.202161 TGTTCTCCTCCTGATTATTCTCGC 60.202 45.833 0.00 0.00 0.00 5.03
1286 1345 1.143305 CTGATTATTCTCGCCCGCTG 58.857 55.000 0.00 0.00 0.00 5.18
1291 1351 4.021807 TGATTATTCTCGCCCGCTGTAATA 60.022 41.667 0.00 0.00 0.00 0.98
1401 1461 3.129287 CCATTCCTGTCAAACTGGTATGC 59.871 47.826 13.53 0.00 40.82 3.14
1407 1467 2.147958 GTCAAACTGGTATGCGTTCCA 58.852 47.619 4.03 4.03 0.00 3.53
1443 1503 2.493973 CCTCTCTCGTGCCTCAGC 59.506 66.667 0.00 0.00 40.48 4.26
1460 1520 5.107220 GCCTCAGCAATTCAACTGATTTTTG 60.107 40.000 3.50 0.00 41.84 2.44
1463 1523 5.070180 TCAGCAATTCAACTGATTTTTGGGA 59.930 36.000 0.00 0.00 37.99 4.37
1552 1613 5.577945 AGAAAAATAATGTGATGCCTTTGCG 59.422 36.000 0.00 0.00 41.78 4.85
1661 1731 4.202151 ACAACCCATTGCTTCTTGTTCTTC 60.202 41.667 0.00 0.00 39.66 2.87
1662 1732 3.837355 ACCCATTGCTTCTTGTTCTTCT 58.163 40.909 0.00 0.00 0.00 2.85
1843 1917 3.606662 GCGGAGGAGAGCGCCATA 61.607 66.667 2.29 0.00 0.00 2.74
1888 1962 2.433318 GACGTGGTGCTCAGGCTC 60.433 66.667 0.00 0.00 39.59 4.70
1897 1971 1.739562 GCTCAGGCTCAGGAACGTG 60.740 63.158 0.00 0.00 35.22 4.49
1970 2044 0.530288 GGGCGCATCAGGCTTTTAAA 59.470 50.000 10.83 0.00 41.67 1.52
1971 2045 1.136891 GGGCGCATCAGGCTTTTAAAT 59.863 47.619 10.83 0.00 41.67 1.40
1972 2046 2.418609 GGGCGCATCAGGCTTTTAAATT 60.419 45.455 10.83 0.00 41.67 1.82
1973 2047 2.860136 GGCGCATCAGGCTTTTAAATTC 59.140 45.455 10.83 0.00 41.67 2.17
1974 2048 2.860136 GCGCATCAGGCTTTTAAATTCC 59.140 45.455 0.30 0.00 41.67 3.01
1975 2049 3.675775 GCGCATCAGGCTTTTAAATTCCA 60.676 43.478 0.30 0.00 41.67 3.53
1979 2053 6.925165 CGCATCAGGCTTTTAAATTCCATAAT 59.075 34.615 8.42 0.00 41.67 1.28
1981 2055 9.762933 GCATCAGGCTTTTAAATTCCATAATTA 57.237 29.630 8.42 0.00 40.25 1.40
1985 2059 9.468532 CAGGCTTTTAAATTCCATAATTAGCTC 57.531 33.333 0.00 0.00 35.05 4.09
2193 2276 1.404391 CATCCTCCTTGCTTGATGTGC 59.596 52.381 0.00 0.00 32.00 4.57
2216 2299 1.505477 GCATCTGCAATCCGGAGAGC 61.505 60.000 20.63 20.63 46.30 4.09
2236 2319 2.165030 GCAAAGGCTACAATGTGCTGAT 59.835 45.455 0.00 0.00 36.96 2.90
2247 2330 0.397564 TGTGCTGATCAGTCTTGGCA 59.602 50.000 23.38 12.41 0.00 4.92
2308 2391 2.223340 GGGTGATTAATCGCAGTTGCAG 60.223 50.000 25.97 0.00 42.21 4.41
2333 2416 4.914983 TCGAAGAGTAGGTCTGGTTTCTA 58.085 43.478 0.00 0.00 34.84 2.10
2345 2428 6.943146 AGGTCTGGTTTCTAAAGGAGAATTTC 59.057 38.462 0.00 0.00 43.84 2.17
2387 2470 1.469703 TGCGGTGATCTTGATTTGCAG 59.530 47.619 0.00 0.00 0.00 4.41
2414 2497 4.829064 AACGATATGCAACTTGTGTGTT 57.171 36.364 0.00 0.00 0.00 3.32
2432 2515 2.664568 TGTTTAGACGCGTAATGCTCAC 59.335 45.455 13.97 6.37 43.27 3.51
2446 2529 0.861837 GCTCACAGACTTGAACACCG 59.138 55.000 0.00 0.00 0.00 4.94
2457 2540 1.295792 TGAACACCGTCTTGACTTGC 58.704 50.000 0.00 0.00 0.00 4.01
2464 2547 1.056103 CGTCTTGACTTGCTCGTCAG 58.944 55.000 8.30 4.72 44.02 3.51
2475 2558 1.975363 GCTCGTCAGACCATGCTTGC 61.975 60.000 0.00 0.00 0.00 4.01
2484 2567 5.049818 GTCAGACCATGCTTGCATATTACTC 60.050 44.000 7.84 0.00 0.00 2.59
2492 2575 4.653801 TGCTTGCATATTACTCCCTCTGTA 59.346 41.667 0.00 0.00 0.00 2.74
2594 4629 2.162921 CTGTCCACAGACGCTTTGCG 62.163 60.000 10.49 10.49 46.74 4.85
2614 4649 2.779506 GGGACGATTTTCACAAGACCT 58.220 47.619 0.00 0.00 0.00 3.85
2629 4664 2.747177 AGACCTTGTGATCGATGGGTA 58.253 47.619 0.54 0.00 0.00 3.69
2632 4667 1.538204 CCTTGTGATCGATGGGTACGG 60.538 57.143 0.54 0.00 0.00 4.02
2677 4712 0.881118 GCACATCCCATCGTTTGTGT 59.119 50.000 4.11 0.00 41.14 3.72
2678 4713 2.080693 GCACATCCCATCGTTTGTGTA 58.919 47.619 4.11 0.00 41.14 2.90
2679 4714 2.095853 GCACATCCCATCGTTTGTGTAG 59.904 50.000 4.11 0.00 41.14 2.74
2680 4715 2.095853 CACATCCCATCGTTTGTGTAGC 59.904 50.000 0.00 0.00 35.79 3.58
2681 4716 2.290008 ACATCCCATCGTTTGTGTAGCA 60.290 45.455 0.00 0.00 0.00 3.49
2682 4717 2.093306 TCCCATCGTTTGTGTAGCAG 57.907 50.000 0.00 0.00 0.00 4.24
2683 4718 1.346395 TCCCATCGTTTGTGTAGCAGT 59.654 47.619 0.00 0.00 0.00 4.40
2684 4719 2.151202 CCCATCGTTTGTGTAGCAGTT 58.849 47.619 0.00 0.00 0.00 3.16
2685 4720 2.159627 CCCATCGTTTGTGTAGCAGTTC 59.840 50.000 0.00 0.00 0.00 3.01
2686 4721 3.067106 CCATCGTTTGTGTAGCAGTTCT 58.933 45.455 0.00 0.00 0.00 3.01
2710 4745 8.860088 TCTTAGCAGTTCTCTTATGCATATGTA 58.140 33.333 16.67 0.00 42.45 2.29
2738 4773 5.696724 CAGAACTCAGACCATTACGAAAAGT 59.303 40.000 0.00 0.00 0.00 2.66
2861 4900 9.276590 CTCATCATGCATTAAACCAGAATAGTA 57.723 33.333 0.00 0.00 0.00 1.82
2881 4920 0.247185 CAATGATGGCAAAACCCGCT 59.753 50.000 0.00 0.00 37.83 5.52
2939 4978 4.512914 GCCTCCCCTGCCATGGAC 62.513 72.222 18.40 7.64 0.00 4.02
2940 4979 4.181010 CCTCCCCTGCCATGGACG 62.181 72.222 18.40 4.66 0.00 4.79
2941 4980 4.864334 CTCCCCTGCCATGGACGC 62.864 72.222 18.40 0.00 0.00 5.19
2943 4982 4.864334 CCCCTGCCATGGACGCTC 62.864 72.222 18.40 0.00 0.00 5.03
2946 4985 4.147449 CTGCCATGGACGCTCGGA 62.147 66.667 18.40 0.00 0.00 4.55
2947 4986 4.451150 TGCCATGGACGCTCGGAC 62.451 66.667 18.40 0.00 0.00 4.79
2949 4988 3.461773 CCATGGACGCTCGGACCT 61.462 66.667 5.56 0.00 0.00 3.85
2950 4989 2.105128 CATGGACGCTCGGACCTC 59.895 66.667 8.57 0.00 0.00 3.85
2951 4990 3.148279 ATGGACGCTCGGACCTCC 61.148 66.667 8.57 0.00 0.00 4.30
2957 4996 3.471806 GCTCGGACCTCCCCCTTC 61.472 72.222 0.00 0.00 0.00 3.46
2958 4997 3.148279 CTCGGACCTCCCCCTTCG 61.148 72.222 0.00 0.00 0.00 3.79
2959 4998 3.959329 CTCGGACCTCCCCCTTCGT 62.959 68.421 0.00 0.00 0.00 3.85
2960 4999 3.001406 CGGACCTCCCCCTTCGTT 61.001 66.667 0.00 0.00 0.00 3.85
2961 5000 2.590114 CGGACCTCCCCCTTCGTTT 61.590 63.158 0.00 0.00 0.00 3.60
2962 5001 1.765727 GGACCTCCCCCTTCGTTTT 59.234 57.895 0.00 0.00 0.00 2.43
2963 5002 0.986527 GGACCTCCCCCTTCGTTTTA 59.013 55.000 0.00 0.00 0.00 1.52
2964 5003 1.562942 GGACCTCCCCCTTCGTTTTAT 59.437 52.381 0.00 0.00 0.00 1.40
2965 5004 2.773661 GGACCTCCCCCTTCGTTTTATA 59.226 50.000 0.00 0.00 0.00 0.98
2966 5005 3.393609 GGACCTCCCCCTTCGTTTTATAT 59.606 47.826 0.00 0.00 0.00 0.86
2967 5006 4.141321 GGACCTCCCCCTTCGTTTTATATT 60.141 45.833 0.00 0.00 0.00 1.28
2968 5007 5.072193 GGACCTCCCCCTTCGTTTTATATTA 59.928 44.000 0.00 0.00 0.00 0.98
2969 5008 6.183810 ACCTCCCCCTTCGTTTTATATTAG 57.816 41.667 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.539776 GCAAGCAAAAACCTCACGCG 61.540 55.000 3.53 3.53 0.00 6.01
80 81 6.534634 AGTAATAAATCGCTAGGCAGGAAAT 58.465 36.000 0.00 0.00 0.00 2.17
123 124 6.819397 ATCGCTTTAGCTTTAAGGAAAAGT 57.181 33.333 0.00 0.00 45.46 2.66
127 128 8.556213 TTTAGAATCGCTTTAGCTTTAAGGAA 57.444 30.769 0.00 0.00 39.32 3.36
139 140 5.581126 TCATGCCATTTTAGAATCGCTTT 57.419 34.783 0.00 0.00 31.60 3.51
219 228 1.213013 CGAGTCCGTCTTGACCCAG 59.787 63.158 0.00 0.00 35.83 4.45
220 229 0.611062 ATCGAGTCCGTCTTGACCCA 60.611 55.000 0.00 0.00 39.15 4.51
221 230 0.179134 CATCGAGTCCGTCTTGACCC 60.179 60.000 0.00 0.00 39.15 4.46
229 238 1.141881 GCATGACCATCGAGTCCGT 59.858 57.895 0.00 0.00 35.83 4.69
239 248 2.741517 CACTCGTTTACATGCATGACCA 59.258 45.455 32.75 14.25 0.00 4.02
388 413 5.620654 GCATTTAGCATTTTCTGAGCTGTCA 60.621 40.000 0.00 0.00 44.79 3.58
404 429 0.392461 TGGAGGACACGGCATTTAGC 60.392 55.000 0.00 0.00 44.65 3.09
405 430 1.369625 GTGGAGGACACGGCATTTAG 58.630 55.000 0.00 0.00 40.85 1.85
406 431 3.543884 GTGGAGGACACGGCATTTA 57.456 52.632 0.00 0.00 40.85 1.40
407 432 4.397348 GTGGAGGACACGGCATTT 57.603 55.556 0.00 0.00 40.85 2.32
443 468 3.171528 TGGCCACCAATCAATCAATCAA 58.828 40.909 0.00 0.00 0.00 2.57
444 469 2.817665 TGGCCACCAATCAATCAATCA 58.182 42.857 0.00 0.00 0.00 2.57
471 496 3.751175 TGGTCGAATTTGTCATCAGGAAC 59.249 43.478 0.00 0.00 0.00 3.62
475 500 4.161333 GCTTTGGTCGAATTTGTCATCAG 58.839 43.478 0.00 0.00 0.00 2.90
492 520 2.618241 TGCAAAGTAGAGTGTGGCTTTG 59.382 45.455 10.42 10.42 46.05 2.77
606 634 1.558233 ACTCCCTTCAACTACTCCCG 58.442 55.000 0.00 0.00 0.00 5.14
639 670 9.284594 GCGAAATAGTACTGCATTTTTATTTCA 57.715 29.630 21.16 0.00 37.36 2.69
640 671 8.743099 GGCGAAATAGTACTGCATTTTTATTTC 58.257 33.333 5.39 9.15 35.62 2.17
641 672 7.704899 GGGCGAAATAGTACTGCATTTTTATTT 59.295 33.333 5.39 0.53 0.00 1.40
642 673 7.200455 GGGCGAAATAGTACTGCATTTTTATT 58.800 34.615 5.39 0.00 0.00 1.40
643 674 6.238925 GGGGCGAAATAGTACTGCATTTTTAT 60.239 38.462 5.39 0.00 0.00 1.40
644 675 5.066764 GGGGCGAAATAGTACTGCATTTTTA 59.933 40.000 5.39 0.00 0.00 1.52
645 676 4.142249 GGGGCGAAATAGTACTGCATTTTT 60.142 41.667 5.39 0.00 0.00 1.94
646 677 3.380320 GGGGCGAAATAGTACTGCATTTT 59.620 43.478 5.39 0.35 0.00 1.82
647 678 2.949644 GGGGCGAAATAGTACTGCATTT 59.050 45.455 5.39 4.40 0.00 2.32
648 679 2.572290 GGGGCGAAATAGTACTGCATT 58.428 47.619 5.39 0.00 0.00 3.56
649 680 1.202770 GGGGGCGAAATAGTACTGCAT 60.203 52.381 5.39 0.00 0.00 3.96
650 681 0.179468 GGGGGCGAAATAGTACTGCA 59.821 55.000 5.39 0.00 0.00 4.41
651 682 0.179468 TGGGGGCGAAATAGTACTGC 59.821 55.000 5.39 0.00 0.00 4.40
652 683 2.285977 GTTGGGGGCGAAATAGTACTG 58.714 52.381 5.39 0.00 0.00 2.74
653 684 1.134610 CGTTGGGGGCGAAATAGTACT 60.135 52.381 0.00 0.00 0.00 2.73
664 695 1.468506 AAACACATTCCGTTGGGGGC 61.469 55.000 0.00 0.00 36.01 5.80
680 711 1.271163 TGGGTGTCTCCATCGGAAAAC 60.271 52.381 0.00 0.00 38.11 2.43
704 735 2.341846 TTATCTTGCCGGGTGGATTC 57.658 50.000 2.18 0.00 37.49 2.52
739 770 3.273919 CTGTGCTCCAGTTTTTGCTAC 57.726 47.619 0.00 0.00 36.37 3.58
834 871 3.825014 CCCGCTCCTGCTAAATACTAGTA 59.175 47.826 4.77 4.77 36.97 1.82
835 872 2.628657 CCCGCTCCTGCTAAATACTAGT 59.371 50.000 0.00 0.00 36.97 2.57
836 873 2.028930 CCCCGCTCCTGCTAAATACTAG 60.029 54.545 0.00 0.00 36.97 2.57
868 905 0.955919 CGTTGCTTTCTCTCCACCCC 60.956 60.000 0.00 0.00 0.00 4.95
907 949 2.016318 TGGTTGAGTTGCAGTTGAGTG 58.984 47.619 0.00 0.00 0.00 3.51
911 953 2.016318 TGACTGGTTGAGTTGCAGTTG 58.984 47.619 0.00 0.00 33.83 3.16
912 954 2.292267 CTGACTGGTTGAGTTGCAGTT 58.708 47.619 0.00 0.00 33.83 3.16
914 956 1.869767 GACTGACTGGTTGAGTTGCAG 59.130 52.381 0.00 0.00 33.83 4.41
915 957 1.806247 CGACTGACTGGTTGAGTTGCA 60.806 52.381 0.00 0.00 33.83 4.08
1134 1188 1.578897 AGGGGAAAAGAGAGGAGCTC 58.421 55.000 4.71 4.71 44.29 4.09
1135 1189 1.912731 GAAGGGGAAAAGAGAGGAGCT 59.087 52.381 0.00 0.00 0.00 4.09
1136 1190 1.912731 AGAAGGGGAAAAGAGAGGAGC 59.087 52.381 0.00 0.00 0.00 4.70
1166 1220 1.485838 GCAGATCGACGGTGCATCTG 61.486 60.000 16.06 16.06 44.39 2.90
1187 1246 2.280708 ACTAAAATTCGCGGAATCGACG 59.719 45.455 6.13 0.00 38.30 5.12
1279 1338 0.941542 TGCGAAATATTACAGCGGGC 59.058 50.000 0.00 0.00 0.00 6.13
1280 1339 2.479837 TCTGCGAAATATTACAGCGGG 58.520 47.619 14.55 7.14 35.14 6.13
1286 1345 6.414890 GTCTTCAGCTTCTGCGAAATATTAC 58.585 40.000 0.00 0.00 45.42 1.89
1291 1351 1.728971 CGTCTTCAGCTTCTGCGAAAT 59.271 47.619 0.00 0.00 45.42 2.17
1323 1383 2.636830 CACTCCGGATTGATGCTCTTT 58.363 47.619 16.44 0.00 0.00 2.52
1401 1461 1.282157 AGGGGGAAAGAGAATGGAACG 59.718 52.381 0.00 0.00 0.00 3.95
1407 1467 3.004000 AGGGAAAAGGGGGAAAGAGAAT 58.996 45.455 0.00 0.00 0.00 2.40
1463 1523 9.158233 TCACGATTCGATTTACTAGGAAATTTT 57.842 29.630 14.25 0.47 0.00 1.82
1472 1532 4.858140 TGCGTTTCACGATTCGATTTACTA 59.142 37.500 13.95 0.00 46.05 1.82
1473 1533 3.676172 TGCGTTTCACGATTCGATTTACT 59.324 39.130 13.95 0.00 46.05 2.24
1474 1534 3.981210 TGCGTTTCACGATTCGATTTAC 58.019 40.909 13.95 4.82 46.05 2.01
1523 1583 8.992835 AAGGCATCACATTATTTTTCTTTCTC 57.007 30.769 0.00 0.00 0.00 2.87
1552 1613 3.132111 TGTTCACCTTCCTTTCCTTTTGC 59.868 43.478 0.00 0.00 0.00 3.68
1661 1731 1.787155 CTTGTCGAACACGTCCTGAAG 59.213 52.381 0.00 0.00 0.00 3.02
1662 1732 1.537348 CCTTGTCGAACACGTCCTGAA 60.537 52.381 0.00 0.00 0.00 3.02
1784 1858 0.468226 ACCAGCTTCTTGACAACCGA 59.532 50.000 0.00 0.00 0.00 4.69
1786 1860 0.312102 GCACCAGCTTCTTGACAACC 59.688 55.000 0.00 0.00 37.91 3.77
1789 1863 4.481195 GGCACCAGCTTCTTGACA 57.519 55.556 0.00 0.00 41.70 3.58
1828 1902 0.533032 GGTATATGGCGCTCTCCTCC 59.467 60.000 7.64 0.04 0.00 4.30
1843 1917 2.423898 CGTGCCCTCGGACAGGTAT 61.424 63.158 0.00 0.00 41.51 2.73
1888 1962 2.738521 CCGCACTCCACGTTCCTG 60.739 66.667 0.00 0.00 0.00 3.86
1918 1992 1.520342 GTCGATCCACTGGAGCTGC 60.520 63.158 11.54 0.00 35.75 5.25
1970 2044 6.043012 AGAGAGTGCAGAGCTAATTATGGAAT 59.957 38.462 0.00 0.00 0.00 3.01
1971 2045 5.365025 AGAGAGTGCAGAGCTAATTATGGAA 59.635 40.000 0.00 0.00 0.00 3.53
1972 2046 4.898265 AGAGAGTGCAGAGCTAATTATGGA 59.102 41.667 0.00 0.00 0.00 3.41
1973 2047 4.989797 CAGAGAGTGCAGAGCTAATTATGG 59.010 45.833 0.00 0.00 0.00 2.74
2000 2074 3.497640 CACTTGAGAAAGAACTCTGCAGG 59.502 47.826 15.13 7.28 37.73 4.85
2001 2075 4.375272 TCACTTGAGAAAGAACTCTGCAG 58.625 43.478 7.63 7.63 37.73 4.41
2205 2288 4.645809 GCCTTTGCTCTCCGGATT 57.354 55.556 3.57 0.00 33.53 3.01
2216 2299 3.441222 TGATCAGCACATTGTAGCCTTTG 59.559 43.478 0.00 2.03 0.00 2.77
2236 2319 2.151202 GTTCGGAAATGCCAAGACTGA 58.849 47.619 0.00 0.00 35.94 3.41
2247 2330 0.966179 GGCAACCAAGGTTCGGAAAT 59.034 50.000 0.51 0.00 36.00 2.17
2298 2381 0.737367 TCTTCGATCCTGCAACTGCG 60.737 55.000 0.00 0.00 45.83 5.18
2308 2391 2.657143 ACCAGACCTACTCTTCGATCC 58.343 52.381 0.00 0.00 0.00 3.36
2345 2428 5.237127 GCAGAAATTTCCCTGAAACAAAAGG 59.763 40.000 14.61 0.00 34.23 3.11
2387 2470 0.575390 AGTTGCATATCGTTACGCGC 59.425 50.000 5.73 0.00 41.07 6.86
2408 2491 2.754478 GCATTACGCGTCTAAACACAC 58.246 47.619 18.63 0.00 0.00 3.82
2432 2515 2.540101 GTCAAGACGGTGTTCAAGTCTG 59.460 50.000 11.02 7.38 43.60 3.51
2457 2540 0.671472 TGCAAGCATGGTCTGACGAG 60.671 55.000 0.00 0.00 0.00 4.18
2464 2547 3.503748 GGGAGTAATATGCAAGCATGGTC 59.496 47.826 17.26 6.59 37.82 4.02
2594 4629 2.779506 AGGTCTTGTGAAAATCGTCCC 58.220 47.619 0.00 0.00 0.00 4.46
2609 4644 1.573108 ACCCATCGATCACAAGGTCT 58.427 50.000 0.00 0.00 0.00 3.85
2614 4649 0.179094 GCCGTACCCATCGATCACAA 60.179 55.000 0.00 0.00 0.00 3.33
2632 4667 2.203294 ACCTTGGTTCACGTGGGC 60.203 61.111 17.00 8.69 0.00 5.36
2637 4672 2.226437 CCTGATTTCACCTTGGTTCACG 59.774 50.000 0.00 0.00 0.00 4.35
2645 4680 2.450476 GGATGTGCCTGATTTCACCTT 58.550 47.619 0.00 0.00 32.51 3.50
2677 4712 5.730296 AAGAGAACTGCTAAGAACTGCTA 57.270 39.130 0.00 0.00 0.00 3.49
2678 4713 4.615588 AAGAGAACTGCTAAGAACTGCT 57.384 40.909 0.00 0.00 0.00 4.24
2679 4714 5.220567 GCATAAGAGAACTGCTAAGAACTGC 60.221 44.000 0.00 0.00 33.15 4.40
2680 4715 5.871524 TGCATAAGAGAACTGCTAAGAACTG 59.128 40.000 0.00 0.00 36.84 3.16
2681 4716 6.042638 TGCATAAGAGAACTGCTAAGAACT 57.957 37.500 0.00 0.00 36.84 3.01
2682 4717 6.917217 ATGCATAAGAGAACTGCTAAGAAC 57.083 37.500 0.00 0.00 36.84 3.01
2683 4718 8.206867 ACATATGCATAAGAGAACTGCTAAGAA 58.793 33.333 15.50 0.00 36.84 2.52
2684 4719 7.730084 ACATATGCATAAGAGAACTGCTAAGA 58.270 34.615 15.50 0.00 36.84 2.10
2685 4720 7.959689 ACATATGCATAAGAGAACTGCTAAG 57.040 36.000 15.50 0.00 36.84 2.18
2710 4745 6.037786 TCGTAATGGTCTGAGTTCTGAATT 57.962 37.500 0.00 0.00 0.00 2.17
2716 4751 6.310711 CCTACTTTTCGTAATGGTCTGAGTTC 59.689 42.308 0.00 0.00 0.00 3.01
2738 4773 6.737720 ATGTAGTCTTCAATCTCATGCCTA 57.262 37.500 0.00 0.00 0.00 3.93
2861 4900 0.037419 GCGGGTTTTGCCATCATTGT 60.037 50.000 0.00 0.00 39.65 2.71
2881 4920 2.557056 AGTTCAAGATTCGACGACCTCA 59.443 45.455 0.00 0.00 0.00 3.86
2940 4979 3.471806 GAAGGGGGAGGTCCGAGC 61.472 72.222 0.00 0.00 36.71 5.03
2941 4980 3.148279 CGAAGGGGGAGGTCCGAG 61.148 72.222 0.00 0.00 36.71 4.63
2942 4981 3.534704 AACGAAGGGGGAGGTCCGA 62.535 63.158 0.00 0.00 36.71 4.55
2943 4982 2.120737 AAAACGAAGGGGGAGGTCCG 62.121 60.000 0.00 0.00 36.71 4.79
2944 4983 0.986527 TAAAACGAAGGGGGAGGTCC 59.013 55.000 0.00 0.00 0.00 4.46
2945 4984 4.701651 ATATAAAACGAAGGGGGAGGTC 57.298 45.455 0.00 0.00 0.00 3.85
2946 4985 6.183810 CTAATATAAAACGAAGGGGGAGGT 57.816 41.667 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.