Multiple sequence alignment - TraesCS7D01G319100

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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 TraesCS7D01G319100 chr7D 100.000 4572 0 0 1 4572 407853272 407848701 0.000000e+00 8444
1 TraesCS7D01G319100 chr7A 93.545 3269 126 32 1 3235 466250790 466247573 0.000000e+00 4789
2 TraesCS7D01G319100 chr7A 94.209 1347 47 10 3245 4572 466247527 466246193 0.000000e+00 2026
3 TraesCS7D01G319100 chr7B 92.086 2363 116 30 905 3235 419038203 419035880 0.000000e+00 3262
4 TraesCS7D01G319100 chr7B 95.139 1296 45 8 3284 4572 419035780 419034496 0.000000e+00 2028
5 TraesCS7D01G319100 chr7B 92.377 551 17 9 1 546 419039199 419038669 0.000000e+00 761
6 TraesCS7D01G319100 chr7B 89.744 195 10 5 653 839 419038568 419038376 1.640000e-59 241
7 TraesCS7D01G319100 chr6A 92.974 427 24 5 3949 4371 265993261 265993685 6.500000e-173 617
8 TraesCS7D01G319100 chr6A 93.204 103 7 0 4376 4478 265993777 265993879 7.920000e-33 152


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 TraesCS7D01G319100 chr7D 407848701 407853272 4571 True 8444.0 8444 100.0000 1 4572 1 chr7D.!!$R1 4571
1 TraesCS7D01G319100 chr7A 466246193 466250790 4597 True 3407.5 4789 93.8770 1 4572 2 chr7A.!!$R1 4571
2 TraesCS7D01G319100 chr7B 419034496 419039199 4703 True 1573.0 3262 92.3365 1 4572 4 chr7B.!!$R1 4571
3 TraesCS7D01G319100 chr6A 265993261 265993879 618 False 384.5 617 93.0890 3949 4478 2 chr6A.!!$F1 529

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
365 366 4.543590 TTTTTGTTGGGAGCAAACAGAA 57.456 36.364 0.00 0.0 38.67 3.02 F
1077 1251 1.280746 GTCCTTGTCGTCGTCGTCA 59.719 57.895 1.33 0.0 38.33 4.35 F
1736 1924 0.105964 GGTACATACTGATGCGGCCA 59.894 55.000 2.24 0.0 36.43 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1500 1680 0.461961 CCCATTCCGAGAGTCCTCAC 59.538 60.0 0.0 0.0 39.39 3.51 R
2373 2565 0.179001 CCGGTTTTCCTGGAGGTGTT 60.179 55.0 0.0 0.0 36.32 3.32 R
3645 3899 0.653323 CAACACAAACCGAGTTCGCG 60.653 55.0 0.0 0.0 38.18 5.87 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
278 279 7.119116 ACAGATTGCTACAACATTCGTCAATTA 59.881 33.333 0.00 0.00 0.00 1.40
365 366 4.543590 TTTTTGTTGGGAGCAAACAGAA 57.456 36.364 0.00 0.00 38.67 3.02
606 616 7.041644 TCGTTGAGTTATTTGGTACTTCCTTTG 60.042 37.037 0.00 0.00 37.07 2.77
777 814 6.044682 GCTGTGCTAATCCTAATGCAAAAAT 58.955 36.000 0.00 0.00 37.17 1.82
1077 1251 1.280746 GTCCTTGTCGTCGTCGTCA 59.719 57.895 1.33 0.00 38.33 4.35
1272 1447 3.133003 TCCTTCTTCCCGCTAGAGATTTG 59.867 47.826 0.00 0.00 0.00 2.32
1290 1465 3.703001 TTGGATGAACTCCCTCTGTTC 57.297 47.619 0.00 0.00 44.23 3.18
1291 1466 1.550524 TGGATGAACTCCCTCTGTTCG 59.449 52.381 0.00 0.00 44.67 3.95
1292 1467 1.646189 GATGAACTCCCTCTGTTCGC 58.354 55.000 0.00 0.00 44.67 4.70
1344 1519 8.443937 ACAAGAGAAATTTCTAGTAAACGATGC 58.556 33.333 20.51 4.09 37.73 3.91
1345 1520 8.660373 CAAGAGAAATTTCTAGTAAACGATGCT 58.340 33.333 20.51 6.28 37.73 3.79
1352 1527 5.236655 TCTAGTAAACGATGCTCTGACTG 57.763 43.478 0.00 0.00 0.00 3.51
1429 1609 7.839680 ACAAAAGGGGAATGGATGATTATAC 57.160 36.000 0.00 0.00 0.00 1.47
1500 1680 0.392193 GGGTCTGCATCCTGTGACTG 60.392 60.000 7.78 0.00 0.00 3.51
1536 1716 1.271840 GGGGTGTCACAGCTCCCATA 61.272 60.000 6.99 0.00 42.38 2.74
1537 1717 0.839946 GGGTGTCACAGCTCCCATAT 59.160 55.000 6.99 0.00 40.79 1.78
1541 1721 1.210234 TGTCACAGCTCCCATATGTGG 59.790 52.381 0.51 0.51 43.54 4.17
1566 1753 9.342308 GGATCCTAATGTTTTTATCTGACATGA 57.658 33.333 3.84 0.00 34.47 3.07
1625 1813 1.938577 CTCCATGTCATGAAAGGCGAG 59.061 52.381 14.67 7.18 0.00 5.03
1721 1909 3.556513 CGCTGAGATCGTCAATAGGTAC 58.443 50.000 0.00 0.00 33.60 3.34
1726 1914 6.072397 GCTGAGATCGTCAATAGGTACATACT 60.072 42.308 0.00 0.00 33.60 2.12
1732 1920 4.617223 CGTCAATAGGTACATACTGATGCG 59.383 45.833 5.41 0.82 36.43 4.73
1735 1923 0.393077 AGGTACATACTGATGCGGCC 59.607 55.000 0.00 0.00 36.43 6.13
1736 1924 0.105964 GGTACATACTGATGCGGCCA 59.894 55.000 2.24 0.00 36.43 5.36
1737 1925 1.502231 GTACATACTGATGCGGCCAG 58.498 55.000 2.24 0.62 36.43 4.85
1744 1932 0.813184 CTGATGCGGCCAGAAACAAT 59.187 50.000 2.24 0.00 33.65 2.71
1746 1934 2.423185 CTGATGCGGCCAGAAACAATAA 59.577 45.455 2.24 0.00 33.65 1.40
1747 1935 2.163412 TGATGCGGCCAGAAACAATAAC 59.837 45.455 2.24 0.00 0.00 1.89
1748 1936 1.610363 TGCGGCCAGAAACAATAACA 58.390 45.000 2.24 0.00 0.00 2.41
1750 1938 2.030363 TGCGGCCAGAAACAATAACAAG 60.030 45.455 2.24 0.00 0.00 3.16
1751 1939 2.595386 CGGCCAGAAACAATAACAAGC 58.405 47.619 2.24 0.00 0.00 4.01
1809 1997 4.009675 CAACACCTGCTTAGGCTGATAAA 58.990 43.478 5.24 0.00 39.31 1.40
1816 2004 5.247110 CCTGCTTAGGCTGATAAATAGAGGA 59.753 44.000 5.24 0.00 39.31 3.71
1856 2044 2.747855 GGCCCCTTGAGAGTTGCG 60.748 66.667 0.00 0.00 0.00 4.85
1907 2095 7.839907 TGGATTTCCATCTGATTACCTTTTTG 58.160 34.615 0.00 0.00 42.01 2.44
1961 2149 0.817654 GGGTAAAGCATGGAAGCACC 59.182 55.000 0.00 0.00 36.85 5.01
1972 2160 0.745845 GGAAGCACCATCATCAGCGT 60.746 55.000 0.00 0.00 38.79 5.07
1998 2187 6.500684 TTCACTTATCCAACTTTCTGATGC 57.499 37.500 0.00 0.00 0.00 3.91
2009 2198 3.005155 ACTTTCTGATGCTGGTTTTCTGC 59.995 43.478 0.00 0.00 40.23 4.26
2024 2213 7.607250 TGGTTTTCTGCAATTAATCGGTTATT 58.393 30.769 0.00 0.00 0.00 1.40
2025 2214 8.740906 TGGTTTTCTGCAATTAATCGGTTATTA 58.259 29.630 0.00 0.00 0.00 0.98
2053 2244 4.937201 AAAAATGAACAGGTTCCCAGTC 57.063 40.909 9.49 0.00 38.77 3.51
2147 2338 3.384789 TCTGGATCAGACCATCCTTTACG 59.615 47.826 0.00 0.00 42.79 3.18
2232 2424 3.118261 ACCTCTGTGAGTCTTTCTTTGCA 60.118 43.478 0.00 0.00 0.00 4.08
2256 2448 7.567571 CATATAATCGTGCTAAAGGAACACTG 58.432 38.462 0.00 0.00 32.07 3.66
2296 2488 0.110823 GTTTCTACGCAGCAACGGTG 60.111 55.000 0.00 0.00 37.37 4.94
2312 2504 6.319658 AGCAACGGTGATTTGAGAATATTCAT 59.680 34.615 17.56 2.12 0.00 2.57
2339 2531 5.237561 ACATACTCTATCGCTAGTGTCACAG 59.762 44.000 5.62 2.18 34.44 3.66
2344 2536 6.990939 ACTCTATCGCTAGTGTCACAGTATAA 59.009 38.462 5.62 0.00 27.96 0.98
2371 2563 8.746922 ATTATTGTAGTGTTGCTGATGTTTTG 57.253 30.769 0.00 0.00 0.00 2.44
2372 2564 5.826601 TTGTAGTGTTGCTGATGTTTTGA 57.173 34.783 0.00 0.00 0.00 2.69
2373 2565 5.826601 TGTAGTGTTGCTGATGTTTTGAA 57.173 34.783 0.00 0.00 0.00 2.69
2375 2567 6.033341 TGTAGTGTTGCTGATGTTTTGAAAC 58.967 36.000 0.00 0.00 39.33 2.78
2391 2584 1.607148 GAAACACCTCCAGGAAAACCG 59.393 52.381 0.00 0.00 38.94 4.44
2421 2614 3.727258 AGTATGGGCGGGCTTGCA 61.727 61.111 0.26 0.00 36.28 4.08
2424 2617 2.977718 TATGGGCGGGCTTGCAGAA 61.978 57.895 0.26 0.00 36.28 3.02
2475 2668 2.367567 AGTTCTTCCTAACTCGTTGCCA 59.632 45.455 0.00 0.00 34.60 4.92
2577 2770 4.507710 GTGATTCAGTAGCAGTGATTGGA 58.492 43.478 0.00 0.00 0.00 3.53
2592 2785 3.400054 GGAGTTGGAGGGGTCGGG 61.400 72.222 0.00 0.00 0.00 5.14
2613 2806 5.010719 CGGGTCAAGGTTAGCTGATATAAGA 59.989 44.000 0.00 0.00 0.00 2.10
2621 2814 9.454859 AAGGTTAGCTGATATAAGAATATTGCC 57.545 33.333 0.00 0.00 32.69 4.52
2622 2815 8.049721 AGGTTAGCTGATATAAGAATATTGCCC 58.950 37.037 0.00 0.00 32.69 5.36
2623 2816 7.829211 GGTTAGCTGATATAAGAATATTGCCCA 59.171 37.037 0.00 0.00 32.69 5.36
2627 2820 8.551440 AGCTGATATAAGAATATTGCCCATACA 58.449 33.333 0.00 0.00 32.69 2.29
2628 2821 9.347240 GCTGATATAAGAATATTGCCCATACAT 57.653 33.333 0.00 0.00 0.00 2.29
2703 2902 3.470709 CGCATCCTCATTACTCCAACAT 58.529 45.455 0.00 0.00 0.00 2.71
2709 2908 4.012374 CCTCATTACTCCAACATTGCAGT 58.988 43.478 0.00 0.00 0.00 4.40
2712 2911 3.641437 TTACTCCAACATTGCAGTTGC 57.359 42.857 12.18 0.00 45.73 4.17
2730 2929 3.893326 TGCTTACAGATAGCAAGAGCA 57.107 42.857 0.00 0.00 45.05 4.26
2742 2941 1.542915 GCAAGAGCATTTGGAGCTTCA 59.457 47.619 0.00 0.00 43.58 3.02
2754 2953 2.224597 TGGAGCTTCAGAAGTCATTGCA 60.225 45.455 11.94 4.54 0.00 4.08
2772 2971 2.169144 TGCAGTGGATGTTCTCGATGAT 59.831 45.455 0.00 0.00 0.00 2.45
2811 3010 1.152756 ACTTGGAGCAACCCACACC 60.153 57.895 0.00 0.00 35.62 4.16
2869 3068 7.174253 GGATCAAGGTATACAACAAGTTTGTGA 59.826 37.037 5.01 0.00 41.31 3.58
2973 3173 1.467734 GCTGTCCAGATGTTGCTTCTG 59.532 52.381 0.00 5.40 40.25 3.02
3223 3423 5.047448 TGCATCTAGCTCCATCAGATTACTC 60.047 44.000 0.00 0.00 45.94 2.59
3235 3435 6.368791 CCATCAGATTACTCTTCGTTTGTTGA 59.631 38.462 0.00 0.00 0.00 3.18
3236 3436 7.065085 CCATCAGATTACTCTTCGTTTGTTGAT 59.935 37.037 0.00 0.00 0.00 2.57
3237 3437 7.351414 TCAGATTACTCTTCGTTTGTTGATG 57.649 36.000 0.00 0.00 0.00 3.07
3238 3438 6.929049 TCAGATTACTCTTCGTTTGTTGATGT 59.071 34.615 0.00 0.00 0.00 3.06
3239 3439 7.441157 TCAGATTACTCTTCGTTTGTTGATGTT 59.559 33.333 0.00 0.00 0.00 2.71
3240 3440 7.742089 CAGATTACTCTTCGTTTGTTGATGTTC 59.258 37.037 0.00 0.00 0.00 3.18
3241 3441 4.452890 ACTCTTCGTTTGTTGATGTTCG 57.547 40.909 0.00 0.00 0.00 3.95
3242 3442 3.869246 ACTCTTCGTTTGTTGATGTTCGT 59.131 39.130 0.00 0.00 0.00 3.85
3291 3543 9.745880 CTCAATTTACTCGTATAGTACCATTGT 57.254 33.333 12.02 0.00 40.48 2.71
3579 3833 5.555017 AGTTGAAATCATGTAGTGCTGACT 58.445 37.500 0.00 0.00 36.07 3.41
3580 3834 5.410746 AGTTGAAATCATGTAGTGCTGACTG 59.589 40.000 0.00 0.00 33.21 3.51
3581 3835 3.686241 TGAAATCATGTAGTGCTGACTGC 59.314 43.478 0.00 0.00 43.25 4.40
3582 3836 3.623906 AATCATGTAGTGCTGACTGCT 57.376 42.857 5.87 0.00 43.37 4.24
3583 3837 2.375173 TCATGTAGTGCTGACTGCTG 57.625 50.000 5.87 0.00 43.37 4.41
3584 3838 1.895131 TCATGTAGTGCTGACTGCTGA 59.105 47.619 5.87 0.00 43.37 4.26
3585 3839 1.998315 CATGTAGTGCTGACTGCTGAC 59.002 52.381 5.87 2.18 43.37 3.51
3602 3856 3.790091 CTGACGAGATGATCATGTGGTT 58.210 45.455 19.21 5.95 0.00 3.67
3607 3861 5.003160 ACGAGATGATCATGTGGTTGAAAA 58.997 37.500 14.30 0.00 0.00 2.29
3638 3892 3.896648 ACAAATAAGAATATGCCGCGG 57.103 42.857 24.05 24.05 0.00 6.46
3661 3915 2.549282 CCGCGAACTCGGTTTGTG 59.451 61.111 8.23 9.39 44.18 3.33
3677 3931 1.229975 TGTGTTGCAGCATGGTCTCG 61.230 55.000 6.50 0.00 35.86 4.04
3756 4010 3.257873 ACAAGGAGATGTCTGTCTCAGTG 59.742 47.826 6.29 5.67 45.12 3.66
3772 4026 5.049818 GTCTCAGTGTGTTCTTCTTTCCATG 60.050 44.000 0.00 0.00 0.00 3.66
3773 4027 5.034852 TCAGTGTGTTCTTCTTTCCATGA 57.965 39.130 0.00 0.00 0.00 3.07
3774 4028 5.624159 TCAGTGTGTTCTTCTTTCCATGAT 58.376 37.500 0.00 0.00 0.00 2.45
3780 4034 9.113838 GTGTGTTCTTCTTTCCATGATACATAT 57.886 33.333 0.00 0.00 0.00 1.78
3896 4150 4.833478 AGCATCAGAAATACCTGACAGT 57.167 40.909 0.93 0.00 44.93 3.55
3936 4192 1.069049 AGGCAATGAAGTTGTGCAACC 59.931 47.619 11.00 0.00 42.06 3.77
3946 4202 2.627699 AGTTGTGCAACCCAAATGTAGG 59.372 45.455 11.00 0.00 42.06 3.18
4146 4404 1.003355 AGCCACATGTCTGGTTCGG 60.003 57.895 0.00 0.00 33.30 4.30
4175 4433 6.200097 GCTTTCTCTGCTTATGAGTTAGCTAC 59.800 42.308 0.00 0.00 38.22 3.58
4238 4496 3.965292 TCTCGATCTCACCGAATACAC 57.035 47.619 0.00 0.00 35.48 2.90
4515 4862 3.689649 GGTATGTGGTAAGCAACTTCTGG 59.310 47.826 0.00 0.00 0.00 3.86
4551 4898 8.910351 AGTTATGATGATTTAGTTCCTTAGCC 57.090 34.615 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
278 279 1.234821 ACACGCACGATGAAACCAAT 58.765 45.000 0.00 0.00 0.00 3.16
365 366 3.011032 ACAAAGGCCTCCAAGAATGATCT 59.989 43.478 5.23 0.00 37.57 2.75
606 616 2.204237 CAAACAAACAAAGAGGCTGCC 58.796 47.619 11.65 11.65 0.00 4.85
777 814 6.708502 TGTTTATTCAACTGCTACTGCACTTA 59.291 34.615 0.00 0.00 44.46 2.24
871 915 6.978080 GCACTCCAACTTTTCATTCAGTTAAA 59.022 34.615 0.00 0.00 31.78 1.52
872 916 6.321181 AGCACTCCAACTTTTCATTCAGTTAA 59.679 34.615 0.00 0.00 31.78 2.01
873 917 5.827797 AGCACTCCAACTTTTCATTCAGTTA 59.172 36.000 0.00 0.00 31.78 2.24
1290 1465 2.520741 GAGAGAGGAGGGGAGGCG 60.521 72.222 0.00 0.00 0.00 5.52
1291 1466 2.123033 GGAGAGAGGAGGGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
1292 1467 2.612251 GGGAGAGAGGAGGGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
1344 1519 0.678395 ACCAGCAGTGTCAGTCAGAG 59.322 55.000 0.00 0.00 0.00 3.35
1345 1520 1.123077 AACCAGCAGTGTCAGTCAGA 58.877 50.000 0.00 0.00 0.00 3.27
1352 1527 2.093447 AGCATACCTAACCAGCAGTGTC 60.093 50.000 0.00 0.00 0.00 3.67
1401 1576 5.903198 TCATCCATTCCCCTTTTGTTTTT 57.097 34.783 0.00 0.00 0.00 1.94
1404 1579 7.014230 CGTATAATCATCCATTCCCCTTTTGTT 59.986 37.037 0.00 0.00 0.00 2.83
1405 1580 6.490040 CGTATAATCATCCATTCCCCTTTTGT 59.510 38.462 0.00 0.00 0.00 2.83
1406 1581 6.570378 GCGTATAATCATCCATTCCCCTTTTG 60.570 42.308 0.00 0.00 0.00 2.44
1429 1609 4.237349 ACTTGTTTAGACAAATTGGGCG 57.763 40.909 0.03 0.00 44.65 6.13
1500 1680 0.461961 CCCATTCCGAGAGTCCTCAC 59.538 60.000 0.00 0.00 39.39 3.51
1536 1716 9.125026 GTCAGATAAAAACATTAGGATCCACAT 57.875 33.333 15.82 1.75 0.00 3.21
1537 1717 8.106462 TGTCAGATAAAAACATTAGGATCCACA 58.894 33.333 15.82 0.00 0.00 4.17
1549 1736 6.712095 AGTTGAGCTCATGTCAGATAAAAACA 59.288 34.615 19.04 0.00 0.00 2.83
1555 1742 5.173664 CACAAGTTGAGCTCATGTCAGATA 58.826 41.667 19.04 0.00 0.00 1.98
1566 1753 0.666913 CAAGCTGCACAAGTTGAGCT 59.333 50.000 23.02 17.01 39.18 4.09
1721 1909 1.331756 GTTTCTGGCCGCATCAGTATG 59.668 52.381 0.00 0.00 36.09 2.39
1726 1914 2.121291 TATTGTTTCTGGCCGCATCA 57.879 45.000 0.00 0.00 0.00 3.07
1732 1920 3.243704 TGTGCTTGTTATTGTTTCTGGCC 60.244 43.478 0.00 0.00 0.00 5.36
1735 1923 4.977963 CAGGTGTGCTTGTTATTGTTTCTG 59.022 41.667 0.00 0.00 0.00 3.02
1736 1924 4.644685 ACAGGTGTGCTTGTTATTGTTTCT 59.355 37.500 0.00 0.00 30.22 2.52
1737 1925 4.932146 ACAGGTGTGCTTGTTATTGTTTC 58.068 39.130 0.00 0.00 30.22 2.78
1744 1932 8.952278 CCTAATAATAAACAGGTGTGCTTGTTA 58.048 33.333 0.00 0.00 42.88 2.41
1746 1934 6.127730 GCCTAATAATAAACAGGTGTGCTTGT 60.128 38.462 0.00 0.00 36.42 3.16
1747 1935 6.095440 AGCCTAATAATAAACAGGTGTGCTTG 59.905 38.462 0.00 0.00 0.00 4.01
1748 1936 6.187682 AGCCTAATAATAAACAGGTGTGCTT 58.812 36.000 0.00 0.00 0.00 3.91
1750 1938 6.451064 AAGCCTAATAATAAACAGGTGTGC 57.549 37.500 0.00 0.00 0.00 4.57
1751 1939 8.739972 AGAAAAGCCTAATAATAAACAGGTGTG 58.260 33.333 0.00 0.00 0.00 3.82
1809 1997 6.305272 TCAATCAAACTGAAGCTCCTCTAT 57.695 37.500 0.00 0.00 0.00 1.98
1816 2004 5.227908 CAAGCATTCAATCAAACTGAAGCT 58.772 37.500 0.00 0.00 38.13 3.74
1856 2044 5.718649 TCTATCTGTGCTGTAAATTTCGC 57.281 39.130 0.00 0.00 0.00 4.70
1907 2095 8.735020 GGAGTTGCAAAAATATTTGAGCACTCC 61.735 40.741 29.78 29.78 46.85 3.85
1961 2149 6.424812 TGGATAAGTGAATAACGCTGATGATG 59.575 38.462 0.00 0.00 39.46 3.07
1962 2150 6.524734 TGGATAAGTGAATAACGCTGATGAT 58.475 36.000 0.00 0.00 39.46 2.45
1969 2157 6.961554 CAGAAAGTTGGATAAGTGAATAACGC 59.038 38.462 0.00 0.00 0.00 4.84
1972 2160 8.677300 GCATCAGAAAGTTGGATAAGTGAATAA 58.323 33.333 0.00 0.00 0.00 1.40
1998 2187 5.059404 ACCGATTAATTGCAGAAAACCAG 57.941 39.130 0.00 0.00 0.00 4.00
2053 2244 0.518636 CTCCAACAACATGACTGCCG 59.481 55.000 0.00 0.00 0.00 5.69
2118 2309 1.198713 GGTCTGATCCAGAGAAGGCA 58.801 55.000 0.00 0.00 41.46 4.75
2154 2346 3.275143 TGAGGTCAAGAAAACGAAGCAA 58.725 40.909 0.00 0.00 0.00 3.91
2160 2352 3.753272 ACATGGATGAGGTCAAGAAAACG 59.247 43.478 0.00 0.00 0.00 3.60
2189 2381 2.852449 TCTTCCTGGCCCTGTATCAAAT 59.148 45.455 0.00 0.00 0.00 2.32
2232 2424 7.272978 ACAGTGTTCCTTTAGCACGATTATAT 58.727 34.615 0.00 0.00 43.55 0.86
2256 2448 1.067354 AGTCGGGTTTCACCATCGTAC 60.067 52.381 0.00 0.00 41.02 3.67
2312 2504 7.281549 TGTGACACTAGCGATAGAGTATGTAAA 59.718 37.037 15.85 0.00 39.76 2.01
2369 2561 3.028130 GGTTTTCCTGGAGGTGTTTCAA 58.972 45.455 0.00 0.00 36.94 2.69
2371 2563 1.607148 CGGTTTTCCTGGAGGTGTTTC 59.393 52.381 0.00 0.00 37.95 2.78
2372 2564 1.687563 CGGTTTTCCTGGAGGTGTTT 58.312 50.000 0.00 0.00 37.95 2.83
2373 2565 0.179001 CCGGTTTTCCTGGAGGTGTT 60.179 55.000 0.00 0.00 36.32 3.32
2375 2567 0.889186 CACCGGTTTTCCTGGAGGTG 60.889 60.000 2.97 15.20 39.85 4.00
2376 2568 1.350310 ACACCGGTTTTCCTGGAGGT 61.350 55.000 2.97 0.00 37.19 3.85
2377 2569 0.688487 TACACCGGTTTTCCTGGAGG 59.312 55.000 2.97 0.00 37.19 4.30
2379 2571 1.129917 TGTACACCGGTTTTCCTGGA 58.870 50.000 2.97 0.00 37.19 3.86
2380 2572 1.810151 CATGTACACCGGTTTTCCTGG 59.190 52.381 2.97 0.00 38.77 4.45
2391 2584 3.463944 GCCCATACTGTACATGTACACC 58.536 50.000 30.31 9.55 40.77 4.16
2421 2614 1.808411 CCGGCACAACACAGTATTCT 58.192 50.000 0.00 0.00 0.00 2.40
2424 2617 1.674322 GGCCGGCACAACACAGTAT 60.674 57.895 30.85 0.00 0.00 2.12
2455 2648 2.762745 TGGCAACGAGTTAGGAAGAAC 58.237 47.619 0.00 0.00 42.51 3.01
2475 2668 4.343526 CCTAGAATGGCTGACTCTGTGTAT 59.656 45.833 0.00 0.00 0.00 2.29
2577 2770 2.606826 GACCCGACCCCTCCAACT 60.607 66.667 0.00 0.00 0.00 3.16
2619 2812 8.734386 CCTTTCTTCAAATAGATATGTATGGGC 58.266 37.037 0.00 0.00 0.00 5.36
2703 2902 3.673902 TGCTATCTGTAAGCAACTGCAA 58.326 40.909 4.22 0.00 46.57 4.08
2712 2911 5.819379 TCCAAATGCTCTTGCTATCTGTAAG 59.181 40.000 0.00 0.00 39.31 2.34
2730 2929 4.082354 GCAATGACTTCTGAAGCTCCAAAT 60.082 41.667 17.00 0.00 0.00 2.32
2742 2941 3.430042 ACATCCACTGCAATGACTTCT 57.570 42.857 0.00 0.00 0.00 2.85
2754 2953 6.227298 AGTTTATCATCGAGAACATCCACT 57.773 37.500 0.00 0.00 0.00 4.00
2772 2971 6.463995 AGTGTTTTTGCATTCTGGAGTTTA 57.536 33.333 0.00 0.00 0.00 2.01
2811 3010 3.479866 CGTCTTCTTTAGCTGCGTTTACG 60.480 47.826 0.00 0.00 43.27 3.18
3223 3423 4.339429 ACAACGAACATCAACAAACGAAG 58.661 39.130 0.00 0.00 0.00 3.79
3235 3435 1.674359 TGTGCCAAGACAACGAACAT 58.326 45.000 0.00 0.00 0.00 2.71
3236 3436 1.674359 ATGTGCCAAGACAACGAACA 58.326 45.000 0.00 0.00 0.00 3.18
3237 3437 4.034048 CCTATATGTGCCAAGACAACGAAC 59.966 45.833 0.00 0.00 0.00 3.95
3238 3438 4.188462 CCTATATGTGCCAAGACAACGAA 58.812 43.478 0.00 0.00 0.00 3.85
3239 3439 3.792401 CCTATATGTGCCAAGACAACGA 58.208 45.455 0.00 0.00 0.00 3.85
3240 3440 2.287915 GCCTATATGTGCCAAGACAACG 59.712 50.000 0.00 0.00 0.00 4.10
3241 3441 3.971032 GCCTATATGTGCCAAGACAAC 57.029 47.619 0.00 0.00 0.00 3.32
3305 3557 8.914011 GCAAGGGAATCCAAGTAAAATTATAGT 58.086 33.333 0.09 0.00 34.83 2.12
3309 3561 7.610865 CAAGCAAGGGAATCCAAGTAAAATTA 58.389 34.615 0.09 0.00 34.83 1.40
3310 3562 6.466812 CAAGCAAGGGAATCCAAGTAAAATT 58.533 36.000 0.09 0.00 34.83 1.82
3325 3579 2.100584 TGTTACACAAAGCAAGCAAGGG 59.899 45.455 0.00 0.00 0.00 3.95
3579 3833 2.482490 CCACATGATCATCTCGTCAGCA 60.482 50.000 4.86 0.00 0.00 4.41
3580 3834 2.133553 CCACATGATCATCTCGTCAGC 58.866 52.381 4.86 0.00 0.00 4.26
3581 3835 3.449528 ACCACATGATCATCTCGTCAG 57.550 47.619 4.86 0.00 0.00 3.51
3582 3836 3.195396 TCAACCACATGATCATCTCGTCA 59.805 43.478 4.86 0.00 0.00 4.35
3583 3837 3.785486 TCAACCACATGATCATCTCGTC 58.215 45.455 4.86 0.00 0.00 4.20
3584 3838 3.893326 TCAACCACATGATCATCTCGT 57.107 42.857 4.86 0.00 0.00 4.18
3585 3839 5.550232 TTTTCAACCACATGATCATCTCG 57.450 39.130 4.86 0.00 0.00 4.04
3602 3856 8.243961 TCTTATTTGTTTGACCCAGATTTTCA 57.756 30.769 0.00 0.00 0.00 2.69
3607 3861 8.416329 GCATATTCTTATTTGTTTGACCCAGAT 58.584 33.333 0.00 0.00 0.00 2.90
3645 3899 0.653323 CAACACAAACCGAGTTCGCG 60.653 55.000 0.00 0.00 38.18 5.87
3661 3915 1.975363 GAGCGAGACCATGCTGCAAC 61.975 60.000 6.36 0.00 42.60 4.17
3677 3931 1.909700 TCCAACACAAATCAGGGAGC 58.090 50.000 0.00 0.00 0.00 4.70
3706 3960 9.715121 AGCACAATAATCTTTCAATCAACAAAT 57.285 25.926 0.00 0.00 0.00 2.32
3707 3961 9.195411 GAGCACAATAATCTTTCAATCAACAAA 57.805 29.630 0.00 0.00 0.00 2.83
3748 4002 4.442706 TGGAAAGAAGAACACACTGAGAC 58.557 43.478 0.00 0.00 0.00 3.36
3756 4010 9.941664 CAATATGTATCATGGAAAGAAGAACAC 57.058 33.333 0.00 0.00 0.00 3.32
3780 4034 7.613801 AGCAAAGTGTATACCCAATATTCACAA 59.386 33.333 0.00 0.00 41.63 3.33
3800 4054 5.528690 TGGCTGCAGAACTATATAAGCAAAG 59.471 40.000 20.43 0.00 0.00 2.77
3811 4065 3.603532 CAGAAATCTGGCTGCAGAACTA 58.396 45.455 20.43 0.00 40.20 2.24
3896 4150 5.012664 TGCCTGTATTTTGTTACTCTGGAGA 59.987 40.000 4.49 0.00 0.00 3.71
3936 4192 3.005684 TGCACTTTTCAGCCTACATTTGG 59.994 43.478 0.00 0.00 0.00 3.28
3946 4202 3.118542 CCTTGAGTTTGCACTTTTCAGC 58.881 45.455 0.00 0.00 31.22 4.26
4175 4433 6.588719 TGATAAGAAAACAGAAATGGTGGG 57.411 37.500 0.00 0.00 0.00 4.61
4238 4496 1.003812 TGGAAATACCACGGTGGAAGG 59.996 52.381 32.72 7.47 44.64 3.46


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

AutoCloner maintained by Alex Coulton.