Multiple sequence alignment - TraesCS5A01G248200

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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 TraesCS5A01G248200 chr5A 100.000 3598 0 0 1 3598 462144087 462147684 0.000000e+00 6645.0
1 TraesCS5A01G248200 chr5B 89.147 3105 171 67 548 3595 427238248 427241243 0.000000e+00 3714.0
2 TraesCS5A01G248200 chr5B 87.220 313 20 8 1 299 427236833 427237139 4.450000e-89 339.0
3 TraesCS5A01G248200 chr5B 86.058 208 15 3 311 517 427237666 427237860 1.010000e-50 211.0
4 TraesCS5A01G248200 chr5D 91.562 2145 99 34 311 2428 361605685 361607774 0.000000e+00 2883.0
5 TraesCS5A01G248200 chr5D 88.267 929 41 25 2701 3597 361609990 361610882 0.000000e+00 1050.0
6 TraesCS5A01G248200 chr5D 88.506 261 15 5 1 252 361604819 361605073 5.840000e-78 302.0
7 TraesCS5A01G248200 chr5D 85.185 243 17 8 2464 2692 361607779 361608016 7.770000e-57 231.0
8 TraesCS5A01G248200 chr4D 88.172 186 22 0 1302 1487 470506936 470507121 4.680000e-54 222.0
9 TraesCS5A01G248200 chr4B 88.172 186 22 0 1302 1487 592819783 592819968 4.680000e-54 222.0
10 TraesCS5A01G248200 chr2D 85.795 176 18 6 1324 1494 557795287 557795114 2.850000e-41 180.0
11 TraesCS5A01G248200 chr6D 86.061 165 23 0 1325 1489 423675471 423675635 1.030000e-40 178.0
12 TraesCS5A01G248200 chr2B 85.714 168 17 6 1324 1486 666089796 666089631 1.720000e-38 171.0
13 TraesCS5A01G248200 chr2B 85.714 168 17 6 1324 1486 666096234 666096069 1.720000e-38 171.0
14 TraesCS5A01G248200 chr2A 85.714 168 17 6 1324 1486 698134341 698134176 1.720000e-38 171.0
15 TraesCS5A01G248200 chr6B 87.805 82 10 0 1580 1661 609887524 609887605 2.960000e-16 97.1
16 TraesCS5A01G248200 chr6A 85.714 77 11 0 1580 1656 552265722 552265798 8.280000e-12 82.4


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 TraesCS5A01G248200 chr5A 462144087 462147684 3597 False 6645.000000 6645 100.000 1 3598 1 chr5A.!!$F1 3597
1 TraesCS5A01G248200 chr5B 427236833 427241243 4410 False 1421.333333 3714 87.475 1 3595 3 chr5B.!!$F1 3594
2 TraesCS5A01G248200 chr5D 361604819 361610882 6063 False 1116.500000 2883 88.380 1 3597 4 chr5D.!!$F1 3596

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
374 952 0.108329 ATGGCGTCGATCCTCGTTTT 60.108 50.0 0.0 0.0 41.35 2.43 F
972 1935 0.114168 TTGGTCATTGGGAGTTGGGG 59.886 55.0 0.0 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 2450 0.170339 GGTCAATGGCGGCTGTTAAC 59.830 55.0 11.43 0.00 0.0 2.01 R
2657 3668 0.586319 ATTGGTTTGCACACGAGTCG 59.414 50.0 11.85 11.85 0.0 4.18 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
40 41 6.455647 TGTACTGAATGTCAAGTAACTCCTG 58.544 40.000 0.00 0.00 0.00 3.86
88 89 2.424733 GGAGAGGGGCGGACACTAC 61.425 68.421 0.00 0.00 0.00 2.73
162 166 7.605410 AGGAAATATAAACAGTACACAACCG 57.395 36.000 0.00 0.00 0.00 4.44
163 167 6.596497 AGGAAATATAAACAGTACACAACCGG 59.404 38.462 0.00 0.00 0.00 5.28
235 241 2.009774 CAAGGATCACGCTGGTAAAGG 58.990 52.381 0.00 0.00 0.00 3.11
266 281 7.604164 AGATATACAAGATGGCTAAACGGATTG 59.396 37.037 0.00 0.00 0.00 2.67
267 282 3.950397 ACAAGATGGCTAAACGGATTGA 58.050 40.909 0.00 0.00 0.00 2.57
268 283 4.331968 ACAAGATGGCTAAACGGATTGAA 58.668 39.130 0.00 0.00 0.00 2.69
269 284 4.949856 ACAAGATGGCTAAACGGATTGAAT 59.050 37.500 0.00 0.00 0.00 2.57
270 285 5.163622 ACAAGATGGCTAAACGGATTGAATG 60.164 40.000 0.00 0.00 0.00 2.67
301 348 9.114952 ACAAAAAGAAAGAGAGAAAAGGTAGAG 57.885 33.333 0.00 0.00 0.00 2.43
303 350 5.414789 AGAAAGAGAGAAAAGGTAGAGCC 57.585 43.478 0.00 0.00 37.58 4.70
371 949 2.722487 GATGGCGTCGATCCTCGT 59.278 61.111 0.00 0.00 41.35 4.18
372 950 1.065928 GATGGCGTCGATCCTCGTT 59.934 57.895 0.00 0.00 41.35 3.85
373 951 0.527817 GATGGCGTCGATCCTCGTTT 60.528 55.000 0.00 0.00 41.35 3.60
374 952 0.108329 ATGGCGTCGATCCTCGTTTT 60.108 50.000 0.00 0.00 41.35 2.43
375 953 0.734942 TGGCGTCGATCCTCGTTTTC 60.735 55.000 0.00 0.00 41.35 2.29
376 954 1.419107 GGCGTCGATCCTCGTTTTCC 61.419 60.000 0.00 0.00 41.35 3.13
377 955 0.458025 GCGTCGATCCTCGTTTTCCT 60.458 55.000 0.00 0.00 41.35 3.36
407 986 0.179062 CTGGAATCGGCAGGAGGAAG 60.179 60.000 0.00 0.00 0.00 3.46
410 989 1.616628 AATCGGCAGGAGGAAGGGT 60.617 57.895 0.00 0.00 0.00 4.34
413 992 1.675641 CGGCAGGAGGAAGGGTTTG 60.676 63.158 0.00 0.00 0.00 2.93
448 1027 0.322277 ATCACCTCAGCACAAGCCAG 60.322 55.000 0.00 0.00 43.56 4.85
493 1072 1.079888 GGAAACCATGCCAAAGCCG 60.080 57.895 0.00 0.00 38.69 5.52
565 1503 1.443802 CCCTTTTCTCTTCACGAGCC 58.556 55.000 0.00 0.00 39.70 4.70
613 1551 2.097791 AGTCGAGACTTTCTCCGTATGC 59.902 50.000 0.00 0.00 40.34 3.14
614 1552 2.097791 GTCGAGACTTTCTCCGTATGCT 59.902 50.000 0.00 0.00 40.34 3.79
637 1578 1.227764 CCCACGAGGCCATGATGAG 60.228 63.158 5.01 0.00 0.00 2.90
742 1683 3.188880 AGCCCTCCCATCAATCAAAAA 57.811 42.857 0.00 0.00 0.00 1.94
796 1753 3.637273 AACACGCCTCCCCCAGTC 61.637 66.667 0.00 0.00 0.00 3.51
819 1776 2.280524 CCGTTTCCCGAGCACACA 60.281 61.111 0.00 0.00 39.56 3.72
822 1779 2.970324 TTTCCCGAGCACACACGC 60.970 61.111 0.00 0.00 0.00 5.34
823 1780 3.741830 TTTCCCGAGCACACACGCA 62.742 57.895 0.00 0.00 0.00 5.24
824 1781 4.662961 TCCCGAGCACACACGCAG 62.663 66.667 0.00 0.00 0.00 5.18
827 1784 3.417224 CGAGCACACACGCAGCAT 61.417 61.111 0.00 0.00 0.00 3.79
828 1785 2.477845 GAGCACACACGCAGCATC 59.522 61.111 0.00 0.00 0.00 3.91
829 1786 2.281002 AGCACACACGCAGCATCA 60.281 55.556 0.00 0.00 0.00 3.07
830 1787 1.642037 GAGCACACACGCAGCATCAT 61.642 55.000 0.00 0.00 0.00 2.45
831 1788 1.210931 GCACACACGCAGCATCATT 59.789 52.632 0.00 0.00 0.00 2.57
832 1789 0.795735 GCACACACGCAGCATCATTC 60.796 55.000 0.00 0.00 0.00 2.67
833 1790 0.518195 CACACACGCAGCATCATTCA 59.482 50.000 0.00 0.00 0.00 2.57
834 1791 0.518636 ACACACGCAGCATCATTCAC 59.481 50.000 0.00 0.00 0.00 3.18
838 1795 1.081892 ACGCAGCATCATTCACTCAC 58.918 50.000 0.00 0.00 0.00 3.51
848 1805 2.028658 TCATTCACTCACTCACAGGAGC 60.029 50.000 0.00 0.00 45.42 4.70
852 1809 1.445754 CTCACTCACAGGAGCGCTG 60.446 63.158 18.48 3.41 45.42 5.18
887 1850 2.372690 CCTTCGCTTCACGTGTCCG 61.373 63.158 16.51 15.79 44.19 4.79
972 1935 0.114168 TTGGTCATTGGGAGTTGGGG 59.886 55.000 0.00 0.00 0.00 4.96
982 1945 0.326618 GGAGTTGGGGGAGAGATCCA 60.327 60.000 0.00 0.00 0.00 3.41
1098 2061 0.394899 GGGGAGCTTGGAATGGTCTG 60.395 60.000 0.00 0.00 38.41 3.51
1104 2067 0.804989 CTTGGAATGGTCTGTTCGGC 59.195 55.000 0.00 0.00 0.00 5.54
1107 2070 2.746277 AATGGTCTGTTCGGCGGC 60.746 61.111 7.21 0.00 0.00 6.53
1486 2449 0.804933 CTCCTACGCGCAAAGGGTAC 60.805 60.000 21.35 0.00 44.73 3.34
1487 2450 2.162754 CCTACGCGCAAAGGGTACG 61.163 63.158 15.62 0.00 44.73 3.67
1524 2489 1.331399 CCTCCTCGACCCCTTTCCTC 61.331 65.000 0.00 0.00 0.00 3.71
1529 2494 1.375523 CGACCCCTTTCCTCGGTTG 60.376 63.158 0.00 0.00 0.00 3.77
1534 2499 2.377531 ACCCCTTTCCTCGGTTGTTTAT 59.622 45.455 0.00 0.00 0.00 1.40
1569 2534 1.536766 TGAAGTGTGTGCTATTGCTGC 59.463 47.619 0.00 0.00 40.48 5.25
1595 2560 1.442148 GTAGGGTGATCAGGCGTCC 59.558 63.158 0.00 0.00 0.00 4.79
1668 2633 3.947132 CTGGAGACGCACAGGCAGG 62.947 68.421 0.00 0.00 41.24 4.85
1751 2719 1.153823 CACCTTCCCGCAGTACTCG 60.154 63.158 0.00 0.00 0.00 4.18
1760 2728 1.946650 GCAGTACTCGATGAGCGCC 60.947 63.158 2.29 0.00 40.61 6.53
1764 2732 2.782222 TACTCGATGAGCGCCACCC 61.782 63.158 2.29 0.00 40.61 4.61
1805 2776 3.774702 GCGAACAACGACGAGGGC 61.775 66.667 0.00 0.00 45.77 5.19
2037 3008 0.037232 GCTCAGCCTCAAGGTACGTT 60.037 55.000 0.00 0.00 37.57 3.99
2038 3009 1.203994 GCTCAGCCTCAAGGTACGTTA 59.796 52.381 0.00 0.00 37.57 3.18
2039 3010 2.877335 CTCAGCCTCAAGGTACGTTAC 58.123 52.381 0.00 0.00 37.57 2.50
2040 3011 1.200716 TCAGCCTCAAGGTACGTTACG 59.799 52.381 2.19 2.19 37.57 3.18
2041 3012 1.068055 CAGCCTCAAGGTACGTTACGT 60.068 52.381 16.31 16.31 38.67 3.57
2098 3083 2.756207 TGTGATATGCATGCATATGGCC 59.244 45.455 43.16 32.07 46.16 5.36
2111 3096 0.044092 TATGGCCCTCAGTCCAAGGA 59.956 55.000 0.00 0.00 35.83 3.36
2128 3113 1.298859 GGAGGTTTACGGCAGCAGTG 61.299 60.000 8.64 0.00 0.00 3.66
2165 3150 3.070018 AGCAATATCATACCGCTTCAGC 58.930 45.455 0.00 0.00 37.78 4.26
2218 3203 4.506288 GCTTTTTGTATTTTGCGTTGTCCT 59.494 37.500 0.00 0.00 0.00 3.85
2219 3204 5.332280 GCTTTTTGTATTTTGCGTTGTCCTC 60.332 40.000 0.00 0.00 0.00 3.71
2257 3242 4.156739 CCAAATTCTCCCAGCTGTTTACTC 59.843 45.833 13.81 0.00 0.00 2.59
2318 3304 0.976641 TCCAGTTGGAATCGCTGTCT 59.023 50.000 0.00 0.00 42.18 3.41
2319 3305 1.347707 TCCAGTTGGAATCGCTGTCTT 59.652 47.619 0.00 0.00 42.18 3.01
2320 3306 2.565391 TCCAGTTGGAATCGCTGTCTTA 59.435 45.455 0.00 0.00 42.18 2.10
2321 3307 2.932614 CCAGTTGGAATCGCTGTCTTAG 59.067 50.000 0.00 0.00 37.39 2.18
2360 3346 3.877508 TGATGAGATCGTACGATGTGAGT 59.122 43.478 33.86 17.48 34.60 3.41
2361 3347 3.946308 TGAGATCGTACGATGTGAGTC 57.054 47.619 33.86 19.44 34.60 3.36
2394 3385 3.261137 CCCTAGGCCTAGTAACAATAGCC 59.739 52.174 33.00 0.00 0.00 3.93
2399 3390 4.227527 AGGCCTAGTAACAATAGCCTTTGT 59.772 41.667 1.29 0.00 41.49 2.83
2525 3526 0.672711 GCCAACTTACCTCCGTGGAC 60.673 60.000 0.00 0.00 39.71 4.02
2567 3568 2.875317 TCAGATCGTCGAGAAGATCCAG 59.125 50.000 19.99 14.93 44.02 3.86
2613 3615 0.833287 TTAGGGCAGCATCTCACCTC 59.167 55.000 0.00 0.00 32.87 3.85
2657 3668 9.110502 ACATTAGTTTATTCTAGCAAGTTAGGC 57.889 33.333 0.00 0.00 0.00 3.93
2754 5732 7.688478 ATGAATTTGTTCATAATGTGCATCG 57.312 32.000 2.04 0.00 39.68 3.84
2755 5733 6.035217 TGAATTTGTTCATAATGTGCATCGG 58.965 36.000 0.00 0.00 0.00 4.18
2756 5734 5.581126 ATTTGTTCATAATGTGCATCGGT 57.419 34.783 0.00 0.00 0.00 4.69
2853 5842 1.727880 CAATGCAATGCTTCCAAACCG 59.272 47.619 6.82 0.00 0.00 4.44
2953 5954 1.745489 GGATCGGGCACTGTTGTCC 60.745 63.158 0.00 0.00 45.05 4.02
3008 6011 3.508840 CCCCGTGAAGCGCCATTC 61.509 66.667 2.29 2.48 39.71 2.67
3062 6066 5.333875 CCTTTTAGTTCCAAACGAGTAGCAC 60.334 44.000 0.00 0.00 36.23 4.40
3072 6076 5.481472 CAAACGAGTAGCACGATTGATTAC 58.519 41.667 0.00 0.00 42.80 1.89
3085 6089 6.423905 CACGATTGATTACATCCTTAATCGGT 59.576 38.462 17.72 4.94 46.41 4.69
3093 6097 9.583765 GATTACATCCTTAATCGGTTATACTCC 57.416 37.037 0.00 0.00 30.66 3.85
3094 6098 8.716674 TTACATCCTTAATCGGTTATACTCCT 57.283 34.615 0.00 0.00 0.00 3.69
3095 6099 6.994221 ACATCCTTAATCGGTTATACTCCTG 58.006 40.000 0.00 0.00 0.00 3.86
3096 6100 6.014499 ACATCCTTAATCGGTTATACTCCTGG 60.014 42.308 0.00 0.00 0.00 4.45
3097 6101 5.708544 TCCTTAATCGGTTATACTCCTGGA 58.291 41.667 0.00 0.00 0.00 3.86
3098 6102 5.773680 TCCTTAATCGGTTATACTCCTGGAG 59.226 44.000 22.00 22.00 35.52 3.86
3099 6103 5.539193 CCTTAATCGGTTATACTCCTGGAGT 59.461 44.000 30.48 30.48 45.54 3.85
3117 6134 6.404074 CCTGGAGTATTTTTCATGTCTTCAGC 60.404 42.308 0.00 0.00 29.98 4.26
3126 6143 1.596260 CATGTCTTCAGCGTGCCATAG 59.404 52.381 0.00 0.00 0.00 2.23
3127 6144 0.608130 TGTCTTCAGCGTGCCATAGT 59.392 50.000 0.00 0.00 0.00 2.12
3130 6147 3.118775 TGTCTTCAGCGTGCCATAGTAAT 60.119 43.478 0.00 0.00 0.00 1.89
3131 6148 3.246226 GTCTTCAGCGTGCCATAGTAATG 59.754 47.826 0.00 0.00 0.00 1.90
3132 6149 3.132111 TCTTCAGCGTGCCATAGTAATGA 59.868 43.478 0.00 0.00 34.84 2.57
3133 6150 2.821546 TCAGCGTGCCATAGTAATGAC 58.178 47.619 0.00 0.00 34.84 3.06
3157 6174 3.135994 GTCCGTTTCTGTAAAGAAGGCA 58.864 45.455 0.00 0.00 0.00 4.75
3179 6196 2.079925 AGCCTTTTAGAGAAAGCAGCG 58.920 47.619 0.00 0.00 0.00 5.18
3211 6228 2.674380 GAACACAGGCCAGGCAGG 60.674 66.667 15.19 6.92 41.84 4.85
3275 6295 2.028567 AGAAGAGAGGAGCTCCAAAACG 60.029 50.000 33.90 0.00 45.10 3.60
3398 6418 3.179443 TGATTGACCGAATAGTGGAGC 57.821 47.619 0.00 0.00 0.00 4.70
3402 6432 2.421739 CCGAATAGTGGAGCGGGG 59.578 66.667 0.00 0.00 40.08 5.73
3403 6433 2.421739 CGAATAGTGGAGCGGGGG 59.578 66.667 0.00 0.00 0.00 5.40
3404 6434 2.111251 GAATAGTGGAGCGGGGGC 59.889 66.667 0.00 0.00 0.00 5.80
3405 6435 2.366972 AATAGTGGAGCGGGGGCT 60.367 61.111 0.00 0.00 0.00 5.19
3406 6436 2.666596 GAATAGTGGAGCGGGGGCTG 62.667 65.000 0.00 0.00 0.00 4.85
3502 6532 2.488355 CTTTGCTCCCATGCAGCG 59.512 61.111 9.60 0.00 44.27 5.18
3549 6579 4.433615 TCTGCTCCAATCGATGTAAACTC 58.566 43.478 0.00 0.00 0.00 3.01
3569 6599 0.958876 CGTCCAGGTAAAAGGGTGGC 60.959 60.000 0.00 0.00 0.00 5.01
3571 6601 1.074248 CCAGGTAAAAGGGTGGCGT 59.926 57.895 0.00 0.00 0.00 5.68
3572 6602 0.958876 CCAGGTAAAAGGGTGGCGTC 60.959 60.000 0.00 0.00 0.00 5.19
3573 6603 0.036306 CAGGTAAAAGGGTGGCGTCT 59.964 55.000 0.00 0.00 0.00 4.18
3574 6604 0.323957 AGGTAAAAGGGTGGCGTCTC 59.676 55.000 0.00 0.00 0.00 3.36
3575 6605 0.675837 GGTAAAAGGGTGGCGTCTCC 60.676 60.000 0.00 0.00 0.00 3.71
3576 6606 1.017701 GTAAAAGGGTGGCGTCTCCG 61.018 60.000 1.43 0.00 37.80 4.63
3577 6607 1.474332 TAAAAGGGTGGCGTCTCCGT 61.474 55.000 1.43 0.00 37.80 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.869888 CCAGGAGTTACTTGACATTCAGTAC 59.130 44.000 0.00 0.00 0.00 2.73
40 41 5.048083 TGCTGATGTTCTAATCACAAAACCC 60.048 40.000 0.00 0.00 33.08 4.11
152 156 4.992511 TGCCGGCCGGTTGTGTAC 62.993 66.667 42.53 25.60 37.65 2.90
153 157 3.961838 GATGCCGGCCGGTTGTGTA 62.962 63.158 42.53 22.93 37.65 2.90
163 167 3.204827 AATCGTGCAGATGCCGGC 61.205 61.111 22.73 22.73 40.02 6.13
173 179 3.498082 GTTTTGTGTATCCCAATCGTGC 58.502 45.455 0.00 0.00 0.00 5.34
235 241 7.363431 GTTTAGCCATCTTGTATATCTTTGCC 58.637 38.462 0.00 0.00 0.00 4.52
366 944 2.033194 GGTGCCGAGGAAAACGAGG 61.033 63.158 0.00 0.00 0.00 4.63
367 945 1.004918 AGGTGCCGAGGAAAACGAG 60.005 57.895 0.00 0.00 0.00 4.18
368 946 1.005394 GAGGTGCCGAGGAAAACGA 60.005 57.895 0.00 0.00 0.00 3.85
369 947 2.380410 CGAGGTGCCGAGGAAAACG 61.380 63.158 0.00 0.00 0.00 3.60
370 948 2.677979 GCGAGGTGCCGAGGAAAAC 61.678 63.158 0.00 0.00 37.76 2.43
371 949 2.358247 GCGAGGTGCCGAGGAAAA 60.358 61.111 0.00 0.00 37.76 2.29
390 968 1.147153 CCTTCCTCCTGCCGATTCC 59.853 63.158 0.00 0.00 0.00 3.01
407 986 1.266178 CCTCAACATTCCCCAAACCC 58.734 55.000 0.00 0.00 0.00 4.11
410 989 3.181424 TGATGACCTCAACATTCCCCAAA 60.181 43.478 0.00 0.00 0.00 3.28
413 992 2.369394 GTGATGACCTCAACATTCCCC 58.631 52.381 0.00 0.00 35.07 4.81
483 1062 1.904287 ATGTAACTTCGGCTTTGGCA 58.096 45.000 0.00 0.00 40.87 4.92
493 1072 1.129811 CGGGGCAACGAATGTAACTTC 59.870 52.381 0.00 0.00 35.47 3.01
565 1503 5.149273 CAGTGTTGGAATTTGTTGATCTCG 58.851 41.667 0.00 0.00 0.00 4.04
606 1544 0.174845 TCGTGGGAAAGAGCATACGG 59.825 55.000 0.00 0.00 32.89 4.02
607 1545 1.560923 CTCGTGGGAAAGAGCATACG 58.439 55.000 0.00 0.00 0.00 3.06
613 1551 0.745845 CATGGCCTCGTGGGAAAGAG 60.746 60.000 3.32 0.00 37.23 2.85
614 1552 1.198094 TCATGGCCTCGTGGGAAAGA 61.198 55.000 3.32 0.00 37.23 2.52
655 1596 0.615331 TCGGAGTGGGTCGTACTACT 59.385 55.000 0.00 0.00 0.00 2.57
656 1597 0.729690 GTCGGAGTGGGTCGTACTAC 59.270 60.000 0.00 0.00 0.00 2.73
657 1598 0.615331 AGTCGGAGTGGGTCGTACTA 59.385 55.000 0.00 0.00 0.00 1.82
742 1683 3.639094 GCGAGGGTGCTATATAGGATGAT 59.361 47.826 11.72 0.00 0.00 2.45
819 1776 1.081892 GTGAGTGAATGATGCTGCGT 58.918 50.000 0.00 0.00 0.00 5.24
822 1779 3.332034 TGTGAGTGAGTGAATGATGCTG 58.668 45.455 0.00 0.00 0.00 4.41
823 1780 3.597255 CTGTGAGTGAGTGAATGATGCT 58.403 45.455 0.00 0.00 0.00 3.79
824 1781 2.676839 CCTGTGAGTGAGTGAATGATGC 59.323 50.000 0.00 0.00 0.00 3.91
825 1782 4.182339 CTCCTGTGAGTGAGTGAATGATG 58.818 47.826 0.00 0.00 33.70 3.07
826 1783 3.369261 GCTCCTGTGAGTGAGTGAATGAT 60.369 47.826 0.00 0.00 40.95 2.45
827 1784 2.028658 GCTCCTGTGAGTGAGTGAATGA 60.029 50.000 0.00 0.00 40.95 2.57
828 1785 2.344950 GCTCCTGTGAGTGAGTGAATG 58.655 52.381 0.00 0.00 40.95 2.67
829 1786 2.758736 GCTCCTGTGAGTGAGTGAAT 57.241 50.000 0.00 0.00 40.95 2.57
838 1795 4.079850 AGCCAGCGCTCCTGTGAG 62.080 66.667 7.13 0.00 43.95 3.51
887 1850 4.176752 GTGGCCGGGGATGGAGAC 62.177 72.222 2.18 0.00 0.00 3.36
951 1914 1.895131 CCCAACTCCCAATGACCAAAG 59.105 52.381 0.00 0.00 0.00 2.77
959 1922 0.121197 TCTCTCCCCCAACTCCCAAT 59.879 55.000 0.00 0.00 0.00 3.16
972 1935 0.185416 TACCTCCGGTGGATCTCTCC 59.815 60.000 28.83 0.00 42.45 3.71
982 1945 0.617820 ATGCCTTGTCTACCTCCGGT 60.618 55.000 0.00 0.00 40.16 5.28
989 1952 1.406539 CCAATGCCATGCCTTGTCTAC 59.593 52.381 3.94 0.00 33.51 2.59
991 1954 0.040058 TCCAATGCCATGCCTTGTCT 59.960 50.000 3.94 0.00 33.51 3.41
993 1956 0.974010 CCTCCAATGCCATGCCTTGT 60.974 55.000 3.94 0.00 33.51 3.16
1352 2315 1.535444 TCCTCCGAGTTCTTGGCCA 60.535 57.895 0.00 0.00 0.00 5.36
1455 2418 2.134287 GTAGGAGGGCGGCATGAGA 61.134 63.158 12.47 0.00 0.00 3.27
1486 2449 0.179200 GTCAATGGCGGCTGTTAACG 60.179 55.000 11.43 0.00 0.00 3.18
1487 2450 0.170339 GGTCAATGGCGGCTGTTAAC 59.830 55.000 11.43 0.00 0.00 2.01
1524 2489 4.992319 TGTCAACTACTCCATAAACAACCG 59.008 41.667 0.00 0.00 0.00 4.44
1529 2494 6.929606 ACTTCAGTGTCAACTACTCCATAAAC 59.070 38.462 0.00 0.00 33.79 2.01
1534 2499 4.322080 CACTTCAGTGTCAACTACTCCA 57.678 45.455 0.00 0.00 40.96 3.86
1558 2523 1.835121 CGTAGTACGCAGCAATAGCA 58.165 50.000 10.19 0.00 37.86 3.49
1595 2560 1.658717 GATCGCACCTCCGACGATG 60.659 63.158 1.40 0.00 45.82 3.84
1649 2614 4.687215 TGCCTGTGCGTCTCCAGC 62.687 66.667 0.00 0.00 41.78 4.85
1835 2806 3.202706 GCCGACGGCTTTGATCCC 61.203 66.667 31.30 0.00 46.69 3.85
2037 3008 3.384816 TAGCTAGGCGTGCTACGTA 57.615 52.632 9.72 0.00 44.73 3.57
2038 3009 4.230603 TAGCTAGGCGTGCTACGT 57.769 55.556 9.72 0.00 44.73 3.57
2041 3012 1.471119 ACTTGTAGCTAGGCGTGCTA 58.529 50.000 9.72 9.72 41.46 3.49
2052 3026 2.159037 GCCGGAGTTGTTTACTTGTAGC 59.841 50.000 5.05 0.00 37.17 3.58
2053 3027 3.660865 AGCCGGAGTTGTTTACTTGTAG 58.339 45.455 5.05 0.00 37.17 2.74
2111 3096 1.966451 GCACTGCTGCCGTAAACCT 60.966 57.895 0.00 0.00 37.45 3.50
2128 3113 7.786030 TGATATTGCTAACCAGATATAGAGGC 58.214 38.462 0.00 0.00 0.00 4.70
2165 3150 0.825010 AGGCACCAGCTTGTTTCAGG 60.825 55.000 0.00 0.00 41.70 3.86
2218 3203 2.357034 GGAGGCGTTTGCTGTCGA 60.357 61.111 0.00 0.00 42.25 4.20
2219 3204 1.781025 TTTGGAGGCGTTTGCTGTCG 61.781 55.000 0.00 0.00 42.25 4.35
2257 3242 3.356529 AGGTTTGCTGAGGTCCATTAG 57.643 47.619 0.00 0.00 0.00 1.73
2343 3329 1.598132 CCGACTCACATCGTACGATCT 59.402 52.381 27.24 14.20 40.59 2.75
2432 3423 8.557869 CTAAATTAGCTTGAATGATGCACTTC 57.442 34.615 0.00 0.00 0.00 3.01
2475 3466 2.496871 CCACCTGCAAATATTTCCAGCA 59.503 45.455 12.87 11.47 0.00 4.41
2657 3668 0.586319 ATTGGTTTGCACACGAGTCG 59.414 50.000 11.85 11.85 0.00 4.18
2766 5745 3.576118 ACATGCCTAGCTACTCTACATGG 59.424 47.826 15.52 4.92 36.68 3.66
2828 5817 2.351455 TGGAAGCATTGCATTGCATTG 58.649 42.857 29.40 22.89 43.23 2.82
2829 5818 2.772077 TGGAAGCATTGCATTGCATT 57.228 40.000 29.40 21.15 43.23 3.56
2853 5842 2.880890 TCTCTGCCTTCAACTTTCAAGC 59.119 45.455 0.00 0.00 0.00 4.01
2953 5954 1.294659 GAGGTTGAGGAACAGCAGCG 61.295 60.000 0.00 0.00 33.27 5.18
3008 6011 0.104671 CTGTTGGTGTTTTGGCAGGG 59.895 55.000 0.00 0.00 0.00 4.45
3072 6076 6.210784 TCCAGGAGTATAACCGATTAAGGATG 59.789 42.308 0.00 0.00 34.73 3.51
3092 6096 6.404074 GCTGAAGACATGAAAAATACTCCAGG 60.404 42.308 0.00 0.00 0.00 4.45
3093 6097 6.549952 GCTGAAGACATGAAAAATACTCCAG 58.450 40.000 0.00 0.00 0.00 3.86
3094 6098 5.122239 CGCTGAAGACATGAAAAATACTCCA 59.878 40.000 0.00 0.00 0.00 3.86
3095 6099 5.122396 ACGCTGAAGACATGAAAAATACTCC 59.878 40.000 0.00 0.00 0.00 3.85
3096 6100 6.017933 CACGCTGAAGACATGAAAAATACTC 58.982 40.000 0.00 0.00 0.00 2.59
3097 6101 5.617751 GCACGCTGAAGACATGAAAAATACT 60.618 40.000 0.00 0.00 0.00 2.12
3098 6102 4.554973 GCACGCTGAAGACATGAAAAATAC 59.445 41.667 0.00 0.00 0.00 1.89
3099 6103 4.379394 GGCACGCTGAAGACATGAAAAATA 60.379 41.667 0.00 0.00 0.00 1.40
3100 6104 3.568538 GCACGCTGAAGACATGAAAAAT 58.431 40.909 0.00 0.00 0.00 1.82
3101 6105 2.287547 GGCACGCTGAAGACATGAAAAA 60.288 45.455 0.00 0.00 0.00 1.94
3109 6126 2.579207 TACTATGGCACGCTGAAGAC 57.421 50.000 0.00 0.00 0.00 3.01
3117 6134 3.555956 GGACTTGTCATTACTATGGCACG 59.444 47.826 3.08 0.00 45.57 5.34
3126 6143 6.774354 TTACAGAAACGGACTTGTCATTAC 57.226 37.500 3.08 0.00 0.00 1.89
3127 6144 7.211573 TCTTTACAGAAACGGACTTGTCATTA 58.788 34.615 3.08 0.00 0.00 1.90
3130 6147 5.013568 TCTTTACAGAAACGGACTTGTCA 57.986 39.130 3.08 0.00 0.00 3.58
3131 6148 5.050295 CCTTCTTTACAGAAACGGACTTGTC 60.050 44.000 0.00 0.00 38.63 3.18
3132 6149 4.814771 CCTTCTTTACAGAAACGGACTTGT 59.185 41.667 0.00 0.00 38.63 3.16
3133 6150 4.319549 GCCTTCTTTACAGAAACGGACTTG 60.320 45.833 1.99 0.00 38.63 3.16
3157 6174 3.342719 GCTGCTTTCTCTAAAAGGCTCT 58.657 45.455 0.00 0.00 32.84 4.09
3179 6196 0.032952 TGTTCGTGTCCCTGTGCTAC 59.967 55.000 0.00 0.00 0.00 3.58
3216 6233 2.076100 TCGATTGGCTTTGCAGTACTG 58.924 47.619 18.93 18.93 0.00 2.74
3217 6234 2.472695 TCGATTGGCTTTGCAGTACT 57.527 45.000 0.00 0.00 0.00 2.73
3218 6235 2.223340 CCATCGATTGGCTTTGCAGTAC 60.223 50.000 0.00 0.00 39.09 2.73
3224 6241 1.269413 GGCATCCATCGATTGGCTTTG 60.269 52.381 13.28 9.48 46.01 2.77
3233 6250 2.013563 GCTTGTCTTGGCATCCATCGA 61.014 52.381 0.00 0.00 31.53 3.59
3234 6251 0.379669 GCTTGTCTTGGCATCCATCG 59.620 55.000 0.00 0.00 31.53 3.84
3452 6482 2.277756 GTCCCGTCGGTCGAATCG 60.278 66.667 11.06 0.00 42.86 3.34
3549 6579 0.322187 CCACCCTTTTACCTGGACGG 60.322 60.000 0.00 0.00 39.35 4.79
3571 6601 3.997400 CTCCCAGGCGAGACGGAGA 62.997 68.421 3.66 0.00 43.96 3.71
3572 6602 2.888464 TACTCCCAGGCGAGACGGAG 62.888 65.000 10.96 7.31 46.18 4.63
3573 6603 2.488771 TTACTCCCAGGCGAGACGGA 62.489 60.000 10.96 0.00 33.83 4.69
3574 6604 1.601419 TTTACTCCCAGGCGAGACGG 61.601 60.000 10.96 0.00 33.83 4.79
3575 6605 0.245539 TTTTACTCCCAGGCGAGACG 59.754 55.000 10.96 0.00 33.83 4.18
3576 6606 2.467566 TTTTTACTCCCAGGCGAGAC 57.532 50.000 10.96 0.00 33.83 3.36


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

AutoCloner maintained by Alex Coulton.