Multiple sequence alignment - TraesCS7B01G067600

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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 TraesCS7B01G067600 chr7B 100.000 2384 0 0 1 2384 73009138 73006755 0.000000e+00 4403
1 TraesCS7B01G067600 chr7A 87.343 1430 90 32 19 1384 118454184 118452782 0.000000e+00 1554
2 TraesCS7B01G067600 chr7A 86.641 524 34 15 1810 2329 118451964 118451473 4.480000e-152 547
3 TraesCS7B01G067600 chr7A 95.455 66 3 0 2319 2384 37399959 37400024 3.240000e-19 106
4 TraesCS7B01G067600 chr7D 92.268 388 20 6 1015 1398 113440243 113439862 2.080000e-150 542
5 TraesCS7B01G067600 chr7D 82.609 575 43 24 1702 2274 113429596 113429077 2.790000e-124 455
6 TraesCS7B01G067600 chr7D 86.313 358 19 10 21 352 113440634 113440281 1.740000e-96 363
7 TraesCS7B01G067600 chr7D 86.826 334 24 9 1397 1711 113439823 113439491 2.910000e-94 355
8 TraesCS7B01G067600 chr7D 95.455 66 3 0 2319 2384 38092619 38092684 3.240000e-19 106
9 TraesCS7B01G067600 chr5A 84.293 191 21 3 1625 1814 702458569 702458387 6.770000e-41 178
10 TraesCS7B01G067600 chr5A 95.455 66 2 1 2320 2384 321019548 321019483 1.170000e-18 104
11 TraesCS7B01G067600 chr5A 95.455 66 2 1 2320 2384 692389909 692389844 1.170000e-18 104
12 TraesCS7B01G067600 chr3A 82.517 143 22 3 1674 1814 25407833 25407974 3.220000e-24 122
13 TraesCS7B01G067600 chr3A 95.455 66 2 1 2320 2384 13273437 13273502 1.170000e-18 104
14 TraesCS7B01G067600 chr6B 95.455 66 2 1 2320 2384 603759195 603759260 1.170000e-18 104
15 TraesCS7B01G067600 chr4A 95.455 66 2 1 2320 2384 738865946 738866011 1.170000e-18 104
16 TraesCS7B01G067600 chr2B 91.892 74 4 2 2313 2384 788186683 788186756 4.190000e-18 102
17 TraesCS7B01G067600 chr2D 93.939 66 3 1 2320 2384 129159509 129159444 5.420000e-17 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 TraesCS7B01G067600 chr7B 73006755 73009138 2383 True 4403.0 4403 100.000 1 2384 1 chr7B.!!$R1 2383
1 TraesCS7B01G067600 chr7A 118451473 118454184 2711 True 1050.5 1554 86.992 19 2329 2 chr7A.!!$R1 2310
2 TraesCS7B01G067600 chr7D 113429077 113429596 519 True 455.0 455 82.609 1702 2274 1 chr7D.!!$R1 572
3 TraesCS7B01G067600 chr7D 113439491 113440634 1143 True 420.0 542 88.469 21 1711 3 chr7D.!!$R2 1690

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
509 552 0.107993 AGCTTATCTCGCAGCAAGCA 60.108 50.0 14.87 0.0 44.59 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 2064 0.388907 GCTGCCACGCATTTGTGAAT 60.389 50.0 0.0 0.0 42.55 2.57 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
51 54 6.625362 TGAGCACAACAAAATACTTGTCAAA 58.375 32.000 0.00 0.00 0.00 2.69
174 205 0.541863 CCGATTCCACCCTAGCTGTT 59.458 55.000 0.00 0.00 0.00 3.16
219 250 7.447374 TGTAATGAATTTTGTCGACTCCATT 57.553 32.000 17.92 16.44 0.00 3.16
220 251 7.881142 TGTAATGAATTTTGTCGACTCCATTT 58.119 30.769 17.92 4.20 0.00 2.32
264 295 2.057922 ACAATGAACTCCACCAGTCCT 58.942 47.619 0.00 0.00 32.30 3.85
285 319 4.381292 CCTTTCTGGATCTGTGCAATTTCC 60.381 45.833 0.00 0.00 38.35 3.13
294 328 2.938451 CTGTGCAATTTCCATAGCTCGA 59.062 45.455 0.00 0.00 0.00 4.04
295 329 2.677836 TGTGCAATTTCCATAGCTCGAC 59.322 45.455 0.00 0.00 0.00 4.20
332 367 0.549950 ATGGAGTGGGCTCAATCAGG 59.450 55.000 17.02 0.00 43.37 3.86
333 368 1.225704 GGAGTGGGCTCAATCAGGG 59.774 63.158 17.02 0.00 43.37 4.45
352 387 1.459209 GGGCTTGCGCACATTTTTAAC 59.541 47.619 11.12 0.00 40.09 2.01
404 447 4.467084 GATCAGTTCGCCCGCCCA 62.467 66.667 0.00 0.00 0.00 5.36
405 448 3.757248 GATCAGTTCGCCCGCCCAT 62.757 63.158 0.00 0.00 0.00 4.00
430 473 5.533482 TGATTAAGCTAGCTCGGAATCTTC 58.467 41.667 28.91 16.66 0.00 2.87
444 487 1.927895 ATCTTCGTTTAGCTCAGGCG 58.072 50.000 0.00 0.00 44.37 5.52
449 492 1.810030 GTTTAGCTCAGGCGGTCGG 60.810 63.158 0.00 0.00 44.37 4.79
499 542 2.464865 ACGCATTGTCGAGCTTATCTC 58.535 47.619 7.34 0.00 38.47 2.75
508 551 0.581053 GAGCTTATCTCGCAGCAAGC 59.419 55.000 6.34 6.34 42.92 4.01
509 552 0.107993 AGCTTATCTCGCAGCAAGCA 60.108 50.000 14.87 0.00 44.59 3.91
510 553 0.304098 GCTTATCTCGCAGCAAGCAG 59.696 55.000 9.06 0.00 46.13 4.24
511 554 0.304098 CTTATCTCGCAGCAAGCAGC 59.696 55.000 0.00 0.00 46.13 5.25
520 563 2.488820 GCAAGCAGCTTAGCAGGC 59.511 61.111 18.96 9.93 41.15 4.85
521 564 2.789917 CAAGCAGCTTAGCAGGCG 59.210 61.111 7.52 0.00 36.50 5.52
522 565 1.742880 CAAGCAGCTTAGCAGGCGA 60.743 57.895 7.52 0.00 36.50 5.54
523 566 1.094073 CAAGCAGCTTAGCAGGCGAT 61.094 55.000 7.52 1.99 36.50 4.58
524 567 0.813210 AAGCAGCTTAGCAGGCGATC 60.813 55.000 5.62 0.00 36.50 3.69
525 568 2.593134 GCAGCTTAGCAGGCGATCG 61.593 63.158 11.69 11.69 34.52 3.69
526 569 1.066422 CAGCTTAGCAGGCGATCGA 59.934 57.895 21.57 0.00 34.52 3.59
527 570 0.938637 CAGCTTAGCAGGCGATCGAG 60.939 60.000 21.57 8.82 34.52 4.04
528 571 2.306581 GCTTAGCAGGCGATCGAGC 61.307 63.158 21.57 18.53 0.00 5.03
529 572 1.361993 CTTAGCAGGCGATCGAGCT 59.638 57.895 25.68 25.68 40.92 4.09
530 573 0.662970 CTTAGCAGGCGATCGAGCTC 60.663 60.000 26.00 2.73 38.47 4.09
531 574 2.393989 TTAGCAGGCGATCGAGCTCG 62.394 60.000 30.03 30.03 41.54 5.03
546 589 3.365064 CGAGCTCGATCGGAATAGCTTAA 60.365 47.826 32.06 0.00 45.04 1.85
549 592 3.544285 GCTCGATCGGAATAGCTTAATCG 59.456 47.826 16.41 0.00 37.83 3.34
550 593 4.724303 CTCGATCGGAATAGCTTAATCGT 58.276 43.478 16.41 0.00 37.74 3.73
551 594 5.673068 GCTCGATCGGAATAGCTTAATCGTA 60.673 44.000 16.41 0.00 37.74 3.43
552 595 6.245115 TCGATCGGAATAGCTTAATCGTAA 57.755 37.500 16.41 0.00 37.74 3.18
553 596 6.849502 TCGATCGGAATAGCTTAATCGTAAT 58.150 36.000 16.41 0.00 37.74 1.89
554 597 7.310664 TCGATCGGAATAGCTTAATCGTAATT 58.689 34.615 16.41 0.00 37.74 1.40
572 615 6.147164 TCGTAATTAAGTTCCTCAGCACTTTG 59.853 38.462 0.00 0.00 34.92 2.77
590 633 1.262417 TGGTCTCGCAGTACCATGAA 58.738 50.000 0.00 0.00 39.07 2.57
591 634 1.067142 TGGTCTCGCAGTACCATGAAC 60.067 52.381 0.00 0.00 39.07 3.18
627 670 2.687700 ATGAGTCAGTGGCTTGCTAG 57.312 50.000 0.00 0.00 0.00 3.42
659 702 2.422235 CCTGATTATGGGGGCGTTTGTA 60.422 50.000 0.00 0.00 0.00 2.41
733 797 1.290203 CTCGAACGTTGATGGATGGG 58.710 55.000 5.00 0.00 0.00 4.00
763 827 2.361610 CAATGCCGGCCCTTGAGT 60.362 61.111 26.46 5.44 0.00 3.41
785 849 3.379445 CGTGGGACGCACTACCCT 61.379 66.667 19.15 0.00 45.74 4.34
788 852 1.534476 TGGGACGCACTACCCTTCA 60.534 57.895 0.00 0.00 45.74 3.02
789 853 1.218316 GGGACGCACTACCCTTCAG 59.782 63.158 0.00 0.00 42.56 3.02
790 854 1.218316 GGACGCACTACCCTTCAGG 59.782 63.158 0.00 0.00 43.78 3.86
791 855 1.255667 GGACGCACTACCCTTCAGGA 61.256 60.000 0.00 0.00 39.89 3.86
798 862 3.753797 GCACTACCCTTCAGGAAAAAGAG 59.246 47.826 0.00 0.00 39.89 2.85
819 883 3.447586 AGAAGACGCCATCTAAAGCTGTA 59.552 43.478 0.00 0.00 36.27 2.74
834 898 8.660435 TCTAAAGCTGTATAGGCCATAGATTTT 58.340 33.333 5.01 6.42 30.70 1.82
847 911 9.125026 AGGCCATAGATTTTGTTATCTTTGTAG 57.875 33.333 5.01 0.00 36.34 2.74
888 952 1.068281 CAGATGACGGCAGAGCACTAT 59.932 52.381 0.00 0.00 0.00 2.12
938 1002 3.926527 TCACGTAGCATAGCAAGAAACAG 59.073 43.478 0.00 0.00 0.00 3.16
941 1005 3.553511 CGTAGCATAGCAAGAAACAGGAG 59.446 47.826 0.00 0.00 0.00 3.69
946 1010 4.730657 CATAGCAAGAAACAGGAGCAAAG 58.269 43.478 0.00 0.00 0.00 2.77
947 1011 2.936202 AGCAAGAAACAGGAGCAAAGA 58.064 42.857 0.00 0.00 0.00 2.52
952 1020 4.696479 AGAAACAGGAGCAAAGAAGAGA 57.304 40.909 0.00 0.00 0.00 3.10
1120 1194 2.127869 CGGAGGAAGAGGATGGCGA 61.128 63.158 0.00 0.00 0.00 5.54
1180 1257 1.943730 ATCGGCTGAGAGGAGGAGGT 61.944 60.000 0.00 0.00 0.00 3.85
1188 1265 0.973496 AGAGGAGGAGGTTCTTCGGC 60.973 60.000 0.00 0.00 0.00 5.54
1385 1462 2.651361 CACGGTCGGCTTCTGAGT 59.349 61.111 0.00 0.00 0.00 3.41
1508 1763 8.740906 TGTGTTTTGGTGATTTTTAGTTCTGTA 58.259 29.630 0.00 0.00 0.00 2.74
1526 1781 5.759059 TCTGTATTTGCTTGGATCTCCATT 58.241 37.500 0.00 0.00 46.97 3.16
1600 1858 4.561213 CGTGCGACACAACTATTCTCATTA 59.439 41.667 9.95 0.00 33.40 1.90
1610 1868 7.485913 CACAACTATTCTCATTACATGCAAACC 59.514 37.037 0.00 0.00 0.00 3.27
1613 1871 7.989826 ACTATTCTCATTACATGCAAACCTTC 58.010 34.615 0.00 0.00 0.00 3.46
1618 1876 7.370383 TCTCATTACATGCAAACCTTCTTTTC 58.630 34.615 0.00 0.00 0.00 2.29
1619 1877 6.148948 TCATTACATGCAAACCTTCTTTTCG 58.851 36.000 0.00 0.00 0.00 3.46
1620 1878 5.508200 TTACATGCAAACCTTCTTTTCGT 57.492 34.783 0.00 0.00 0.00 3.85
1621 1879 4.385358 ACATGCAAACCTTCTTTTCGTT 57.615 36.364 0.00 0.00 0.00 3.85
1622 1880 5.508200 ACATGCAAACCTTCTTTTCGTTA 57.492 34.783 0.00 0.00 0.00 3.18
1623 1881 5.278604 ACATGCAAACCTTCTTTTCGTTAC 58.721 37.500 0.00 0.00 0.00 2.50
1724 1985 9.865321 AAAGGATGACAGTTATTGATGAAAATG 57.135 29.630 0.00 0.00 0.00 2.32
1728 1989 6.990798 TGACAGTTATTGATGAAAATGGCAA 58.009 32.000 0.00 0.00 35.90 4.52
1768 2030 4.370917 TCATGCTTTTTCTGAAAACTGCC 58.629 39.130 24.41 12.46 32.51 4.85
1770 2032 3.520569 TGCTTTTTCTGAAAACTGCCAC 58.479 40.909 24.41 10.81 32.51 5.01
1775 2037 0.467290 TCTGAAAACTGCCACCACCC 60.467 55.000 0.00 0.00 0.00 4.61
1776 2038 1.456705 TGAAAACTGCCACCACCCC 60.457 57.895 0.00 0.00 0.00 4.95
1777 2039 1.152546 GAAAACTGCCACCACCCCT 60.153 57.895 0.00 0.00 0.00 4.79
1778 2040 0.111639 GAAAACTGCCACCACCCCTA 59.888 55.000 0.00 0.00 0.00 3.53
1779 2041 0.558712 AAAACTGCCACCACCCCTAA 59.441 50.000 0.00 0.00 0.00 2.69
1780 2042 0.178973 AAACTGCCACCACCCCTAAC 60.179 55.000 0.00 0.00 0.00 2.34
1781 2043 1.357272 AACTGCCACCACCCCTAACA 61.357 55.000 0.00 0.00 0.00 2.41
1782 2044 1.303317 CTGCCACCACCCCTAACAC 60.303 63.158 0.00 0.00 0.00 3.32
1783 2045 1.772567 TGCCACCACCCCTAACACT 60.773 57.895 0.00 0.00 0.00 3.55
1784 2046 1.303317 GCCACCACCCCTAACACTG 60.303 63.158 0.00 0.00 0.00 3.66
1793 2055 1.472480 CCCCTAACACTGAAAATGCCG 59.528 52.381 0.00 0.00 0.00 5.69
1799 2061 2.332654 ACTGAAAATGCCGTCCCGC 61.333 57.895 0.00 0.00 0.00 6.13
1800 2062 3.381169 CTGAAAATGCCGTCCCGCG 62.381 63.158 0.00 0.00 40.95 6.46
1801 2063 4.829518 GAAAATGCCGTCCCGCGC 62.830 66.667 0.00 0.00 39.71 6.86
1842 2331 2.599659 GAACGTTCGTTCGGGATTAGT 58.400 47.619 19.41 0.00 35.77 2.24
1846 2335 2.265683 GTTCGTTCGGGATTAGTGTCC 58.734 52.381 0.00 0.00 37.56 4.02
1847 2336 1.843368 TCGTTCGGGATTAGTGTCCT 58.157 50.000 0.00 0.00 38.38 3.85
1963 2453 5.936686 TCTCTTTCAACTTTGAGATGCAG 57.063 39.130 0.00 0.00 38.61 4.41
2010 2500 5.859205 ATCATCTTTACCAATTCAAGGCC 57.141 39.130 0.00 0.00 0.00 5.19
2012 2502 4.706476 TCATCTTTACCAATTCAAGGCCAG 59.294 41.667 5.01 0.00 0.00 4.85
2030 2520 2.159476 CCAGCCGATTCAACAATCACAG 60.159 50.000 0.00 0.00 38.77 3.66
2033 2523 2.710377 CCGATTCAACAATCACAGGGA 58.290 47.619 0.00 0.00 38.77 4.20
2034 2524 3.282021 CCGATTCAACAATCACAGGGAT 58.718 45.455 0.00 0.00 38.77 3.85
2054 2544 4.218417 GGATGTTGCACCATTGTAAAGAGT 59.782 41.667 0.00 0.00 0.00 3.24
2174 2664 6.037720 TCGTGCAAAAACTCTCTAAATTCACA 59.962 34.615 0.00 0.00 0.00 3.58
2177 2667 8.868916 GTGCAAAAACTCTCTAAATTCACAAAA 58.131 29.630 0.00 0.00 0.00 2.44
2216 2706 7.331026 TCTCACATTGTATACTTTCTTGGGAG 58.669 38.462 4.17 9.82 35.09 4.30
2346 2838 7.639113 TTTTTAGTCCAAACACACTCTCATT 57.361 32.000 0.00 0.00 0.00 2.57
2347 2839 7.639113 TTTTAGTCCAAACACACTCTCATTT 57.361 32.000 0.00 0.00 0.00 2.32
2348 2840 8.740123 TTTTAGTCCAAACACACTCTCATTTA 57.260 30.769 0.00 0.00 0.00 1.40
2349 2841 8.918202 TTTAGTCCAAACACACTCTCATTTAT 57.082 30.769 0.00 0.00 0.00 1.40
2350 2842 8.918202 TTAGTCCAAACACACTCTCATTTATT 57.082 30.769 0.00 0.00 0.00 1.40
2351 2843 7.206981 AGTCCAAACACACTCTCATTTATTG 57.793 36.000 0.00 0.00 0.00 1.90
2352 2844 6.998074 AGTCCAAACACACTCTCATTTATTGA 59.002 34.615 0.00 0.00 0.00 2.57
2353 2845 7.667219 AGTCCAAACACACTCTCATTTATTGAT 59.333 33.333 0.00 0.00 32.72 2.57
2354 2846 7.965107 GTCCAAACACACTCTCATTTATTGATC 59.035 37.037 0.00 0.00 32.72 2.92
2355 2847 7.665145 TCCAAACACACTCTCATTTATTGATCA 59.335 33.333 0.00 0.00 32.72 2.92
2356 2848 8.464404 CCAAACACACTCTCATTTATTGATCAT 58.536 33.333 0.00 0.00 32.72 2.45
2357 2849 9.850628 CAAACACACTCTCATTTATTGATCATT 57.149 29.630 0.00 0.00 32.72 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.422796 TCGCCTTGCATACCCTTAAAAA 58.577 40.909 0.00 0.00 0.00 1.94
4 5 3.074675 TCGCCTTGCATACCCTTAAAA 57.925 42.857 0.00 0.00 0.00 1.52
5 6 2.791347 TCGCCTTGCATACCCTTAAA 57.209 45.000 0.00 0.00 0.00 1.52
6 7 3.290948 AATCGCCTTGCATACCCTTAA 57.709 42.857 0.00 0.00 0.00 1.85
7 8 2.948979 CAAATCGCCTTGCATACCCTTA 59.051 45.455 0.00 0.00 0.00 2.69
8 9 1.750778 CAAATCGCCTTGCATACCCTT 59.249 47.619 0.00 0.00 0.00 3.95
9 10 1.064758 TCAAATCGCCTTGCATACCCT 60.065 47.619 0.00 0.00 0.00 4.34
10 11 1.334869 CTCAAATCGCCTTGCATACCC 59.665 52.381 0.00 0.00 0.00 3.69
11 12 1.268743 GCTCAAATCGCCTTGCATACC 60.269 52.381 0.00 0.00 0.00 2.73
12 13 1.401552 TGCTCAAATCGCCTTGCATAC 59.598 47.619 0.00 0.00 0.00 2.39
13 14 1.401552 GTGCTCAAATCGCCTTGCATA 59.598 47.619 0.00 0.00 32.98 3.14
14 15 0.171903 GTGCTCAAATCGCCTTGCAT 59.828 50.000 0.00 0.00 32.98 3.96
15 16 1.171549 TGTGCTCAAATCGCCTTGCA 61.172 50.000 0.00 0.00 0.00 4.08
16 17 0.039256 TTGTGCTCAAATCGCCTTGC 60.039 50.000 0.00 0.00 0.00 4.01
17 18 1.001487 TGTTGTGCTCAAATCGCCTTG 60.001 47.619 2.18 0.00 35.20 3.61
191 222 8.191446 TGGAGTCGACAAAATTCATTACAAAAA 58.809 29.630 19.50 0.00 0.00 1.94
219 250 9.554724 GTGATCGCTTCAAATTATGAGTTAAAA 57.445 29.630 0.00 0.00 39.77 1.52
220 251 8.726068 TGTGATCGCTTCAAATTATGAGTTAAA 58.274 29.630 7.94 0.00 39.77 1.52
264 295 4.151121 TGGAAATTGCACAGATCCAGAAA 58.849 39.130 5.78 0.00 35.33 2.52
276 310 2.677836 GTGTCGAGCTATGGAAATTGCA 59.322 45.455 0.00 0.00 0.00 4.08
285 319 0.249238 GGAGCCTGTGTCGAGCTATG 60.249 60.000 0.00 0.00 36.87 2.23
318 352 2.440980 GCCCCTGATTGAGCCCAC 60.441 66.667 0.00 0.00 0.00 4.61
332 367 7.427138 TTTTGTTAAAAATGTGCGCAAGCCC 62.427 40.000 14.00 0.00 46.33 5.19
333 368 4.494855 TTTTGTTAAAAATGTGCGCAAGCC 60.495 37.500 14.00 0.00 46.33 4.35
352 387 7.439157 TGACTAGATGACCTGTTCATTTTTG 57.561 36.000 0.00 0.00 45.67 2.44
372 415 4.527509 ACTGATCGTCATTGACTTGACT 57.472 40.909 14.54 0.00 43.10 3.41
388 431 1.768684 ATATGGGCGGGCGAACTGAT 61.769 55.000 0.00 0.00 0.00 2.90
404 447 7.416964 AGATTCCGAGCTAGCTTAATCATAT 57.583 36.000 30.10 18.12 0.00 1.78
405 448 6.842437 AGATTCCGAGCTAGCTTAATCATA 57.158 37.500 30.10 13.82 0.00 2.15
430 473 2.158959 CGACCGCCTGAGCTAAACG 61.159 63.158 0.00 0.00 36.60 3.60
444 487 2.164219 TCTTGGTTATGTACGACCGACC 59.836 50.000 7.96 3.49 38.81 4.79
449 492 7.959109 GGTAAACAAATCTTGGTTATGTACGAC 59.041 37.037 0.56 0.00 43.97 4.34
504 547 1.094073 ATCGCCTGCTAAGCTGCTTG 61.094 55.000 24.35 14.78 0.00 4.01
505 548 0.813210 GATCGCCTGCTAAGCTGCTT 60.813 55.000 19.93 19.93 0.00 3.91
506 549 1.227497 GATCGCCTGCTAAGCTGCT 60.227 57.895 0.00 0.00 0.00 4.24
507 550 2.593134 CGATCGCCTGCTAAGCTGC 61.593 63.158 0.26 0.00 0.00 5.25
508 551 0.938637 CTCGATCGCCTGCTAAGCTG 60.939 60.000 11.09 0.00 0.00 4.24
509 552 1.361993 CTCGATCGCCTGCTAAGCT 59.638 57.895 11.09 0.00 0.00 3.74
510 553 2.306581 GCTCGATCGCCTGCTAAGC 61.307 63.158 11.09 8.65 0.00 3.09
511 554 0.662970 GAGCTCGATCGCCTGCTAAG 60.663 60.000 22.78 10.70 35.76 2.18
512 555 1.360551 GAGCTCGATCGCCTGCTAA 59.639 57.895 22.78 0.87 35.76 3.09
513 556 2.897922 CGAGCTCGATCGCCTGCTA 61.898 63.158 32.06 1.53 43.02 3.49
514 557 4.263209 CGAGCTCGATCGCCTGCT 62.263 66.667 32.06 22.88 43.02 4.24
515 558 4.257510 TCGAGCTCGATCGCCTGC 62.258 66.667 33.84 14.17 44.22 4.85
524 567 0.519519 AGCTATTCCGATCGAGCTCG 59.480 55.000 30.03 30.03 41.40 5.03
525 568 2.715737 AAGCTATTCCGATCGAGCTC 57.284 50.000 24.07 2.73 44.40 4.09
527 570 3.544285 CGATTAAGCTATTCCGATCGAGC 59.456 47.826 18.66 17.30 38.81 5.03
528 571 4.724303 ACGATTAAGCTATTCCGATCGAG 58.276 43.478 18.66 6.95 38.81 4.04
529 572 4.761235 ACGATTAAGCTATTCCGATCGA 57.239 40.909 18.66 0.00 38.81 3.59
530 573 7.507672 AATTACGATTAAGCTATTCCGATCG 57.492 36.000 8.51 8.51 41.34 3.69
543 586 8.038944 AGTGCTGAGGAACTTAATTACGATTAA 58.961 33.333 0.00 0.00 41.55 1.40
546 589 5.978814 AGTGCTGAGGAACTTAATTACGAT 58.021 37.500 0.00 0.00 41.55 3.73
549 592 6.206829 ACCAAAGTGCTGAGGAACTTAATTAC 59.793 38.462 0.00 0.00 40.25 1.89
550 593 6.303839 ACCAAAGTGCTGAGGAACTTAATTA 58.696 36.000 0.00 0.00 40.25 1.40
551 594 5.140454 ACCAAAGTGCTGAGGAACTTAATT 58.860 37.500 0.00 0.00 40.25 1.40
552 595 4.729868 ACCAAAGTGCTGAGGAACTTAAT 58.270 39.130 0.00 0.00 40.25 1.40
553 596 4.134563 GACCAAAGTGCTGAGGAACTTAA 58.865 43.478 0.00 0.00 40.25 1.85
554 597 3.391296 AGACCAAAGTGCTGAGGAACTTA 59.609 43.478 0.00 0.00 40.25 2.24
572 615 1.067142 TGTTCATGGTACTGCGAGACC 60.067 52.381 0.00 0.00 36.17 3.85
627 670 2.163010 CCATAATCAGGATGCGCCAATC 59.837 50.000 4.18 1.21 40.02 2.67
733 797 2.476051 CATTGACCGCTGTGACGC 59.524 61.111 0.00 0.00 0.00 5.19
785 849 3.139077 GGCGTCTTCTCTTTTTCCTGAA 58.861 45.455 0.00 0.00 0.00 3.02
788 852 2.930826 TGGCGTCTTCTCTTTTTCCT 57.069 45.000 0.00 0.00 0.00 3.36
789 853 3.339141 AGATGGCGTCTTCTCTTTTTCC 58.661 45.455 2.64 0.00 31.47 3.13
790 854 6.481954 TTTAGATGGCGTCTTCTCTTTTTC 57.518 37.500 15.53 0.00 38.42 2.29
791 855 5.106515 GCTTTAGATGGCGTCTTCTCTTTTT 60.107 40.000 15.53 0.00 38.42 1.94
798 862 2.622436 ACAGCTTTAGATGGCGTCTTC 58.378 47.619 15.53 2.55 38.42 2.87
819 883 9.646522 ACAAAGATAACAAAATCTATGGCCTAT 57.353 29.630 3.32 0.00 35.10 2.57
843 907 2.289547 GCGGCAGTTGAAGTTTTCTACA 59.710 45.455 0.00 0.00 37.78 2.74
847 911 1.477105 GTGCGGCAGTTGAAGTTTTC 58.523 50.000 1.18 0.00 0.00 2.29
938 1002 1.203523 TCGCTCTCTCTTCTTTGCTCC 59.796 52.381 0.00 0.00 0.00 4.70
941 1005 0.998669 GCTCGCTCTCTCTTCTTTGC 59.001 55.000 0.00 0.00 0.00 3.68
946 1010 1.949525 AGATCAGCTCGCTCTCTCTTC 59.050 52.381 0.00 0.00 0.00 2.87
947 1011 1.949525 GAGATCAGCTCGCTCTCTCTT 59.050 52.381 15.58 0.00 34.03 2.85
968 1036 7.395772 TCAAATCAAAATGTATGCTCAGGGTTA 59.604 33.333 0.00 0.00 0.00 2.85
1158 1232 2.560119 CCTCCTCTCAGCCGATCCG 61.560 68.421 0.00 0.00 0.00 4.18
1159 1233 1.152652 TCCTCCTCTCAGCCGATCC 60.153 63.158 0.00 0.00 0.00 3.36
1160 1234 1.178534 CCTCCTCCTCTCAGCCGATC 61.179 65.000 0.00 0.00 0.00 3.69
1371 1448 0.456995 CGAGAACTCAGAAGCCGACC 60.457 60.000 2.78 0.00 0.00 4.79
1385 1462 3.580904 CCAACAAGGTCGACGAGAA 57.419 52.632 9.92 0.00 0.00 2.87
1526 1781 5.680619 AGAGCCGGATTTTTACATACATGA 58.319 37.500 5.05 0.00 0.00 3.07
1573 1831 1.922570 ATAGTTGTGTCGCACGGATC 58.077 50.000 5.69 0.00 37.14 3.36
1600 1858 4.385358 AACGAAAAGAAGGTTTGCATGT 57.615 36.364 0.00 0.00 0.00 3.21
1610 1868 4.032558 GCCAGGTATCGTAACGAAAAGAAG 59.967 45.833 0.00 0.00 39.99 2.85
1613 1871 2.280708 CGCCAGGTATCGTAACGAAAAG 59.719 50.000 0.00 0.00 39.99 2.27
1618 1876 1.194495 GTTCGCCAGGTATCGTAACG 58.806 55.000 0.00 0.00 0.00 3.18
1619 1877 1.194495 CGTTCGCCAGGTATCGTAAC 58.806 55.000 0.00 0.00 0.00 2.50
1620 1878 0.810648 ACGTTCGCCAGGTATCGTAA 59.189 50.000 0.00 0.00 0.00 3.18
1621 1879 0.810648 AACGTTCGCCAGGTATCGTA 59.189 50.000 0.00 0.00 0.00 3.43
1622 1880 0.457337 GAACGTTCGCCAGGTATCGT 60.457 55.000 13.36 0.00 0.00 3.73
1623 1881 1.469126 CGAACGTTCGCCAGGTATCG 61.469 60.000 34.54 11.07 44.26 2.92
1643 1904 0.389817 CGTTGGGATCTCACTCGCAA 60.390 55.000 0.00 0.12 43.33 4.85
1751 2013 3.865164 GTGGTGGCAGTTTTCAGAAAAAG 59.135 43.478 10.00 7.32 35.10 2.27
1756 2018 0.467290 GGGTGGTGGCAGTTTTCAGA 60.467 55.000 0.00 0.00 0.00 3.27
1768 2030 2.649531 TTTCAGTGTTAGGGGTGGTG 57.350 50.000 0.00 0.00 0.00 4.17
1770 2032 2.231235 GCATTTTCAGTGTTAGGGGTGG 59.769 50.000 0.00 0.00 0.00 4.61
1775 2037 2.161609 GGACGGCATTTTCAGTGTTAGG 59.838 50.000 0.00 0.00 0.00 2.69
1776 2038 2.161609 GGGACGGCATTTTCAGTGTTAG 59.838 50.000 0.00 0.00 0.00 2.34
1777 2039 2.156098 GGGACGGCATTTTCAGTGTTA 58.844 47.619 0.00 0.00 0.00 2.41
1778 2040 0.958822 GGGACGGCATTTTCAGTGTT 59.041 50.000 0.00 0.00 0.00 3.32
1779 2041 2.641197 GGGACGGCATTTTCAGTGT 58.359 52.632 0.00 0.00 0.00 3.55
1793 2055 0.798009 CATTTGTGAATGCGCGGGAC 60.798 55.000 8.83 0.00 36.54 4.46
1801 2063 1.342555 CTGCCACGCATTTGTGAATG 58.657 50.000 0.00 0.00 44.42 2.67
1802 2064 0.388907 GCTGCCACGCATTTGTGAAT 60.389 50.000 0.00 0.00 42.55 2.57
1803 2065 1.007502 GCTGCCACGCATTTGTGAA 60.008 52.632 0.00 0.00 42.55 3.18
1804 2066 2.644418 GCTGCCACGCATTTGTGA 59.356 55.556 0.00 0.00 42.55 3.58
1805 2067 2.730006 TTCGCTGCCACGCATTTGTG 62.730 55.000 0.00 0.00 38.13 3.33
1806 2068 2.551006 TTCGCTGCCACGCATTTGT 61.551 52.632 0.00 0.00 38.13 2.83
1863 2352 2.695359 ACACTTGTAGCGGTTACATGG 58.305 47.619 17.71 11.27 41.72 3.66
1935 2425 8.081025 GCATCTCAAAGTTGAAAGAGAATTCTT 58.919 33.333 9.87 0.00 45.51 2.52
1936 2426 7.230108 TGCATCTCAAAGTTGAAAGAGAATTCT 59.770 33.333 7.95 7.95 40.19 2.40
1937 2427 7.365741 TGCATCTCAAAGTTGAAAGAGAATTC 58.634 34.615 0.00 0.00 40.19 2.17
1938 2428 7.230108 TCTGCATCTCAAAGTTGAAAGAGAATT 59.770 33.333 0.00 0.00 40.19 2.17
1939 2429 6.713903 TCTGCATCTCAAAGTTGAAAGAGAAT 59.286 34.615 0.00 0.00 40.19 2.40
1940 2430 6.057533 TCTGCATCTCAAAGTTGAAAGAGAA 58.942 36.000 0.00 0.00 40.19 2.87
1941 2431 5.614308 TCTGCATCTCAAAGTTGAAAGAGA 58.386 37.500 0.00 0.00 40.96 3.10
1942 2432 5.936686 TCTGCATCTCAAAGTTGAAAGAG 57.063 39.130 0.00 0.00 36.64 2.85
1943 2433 6.713903 AGATTCTGCATCTCAAAGTTGAAAGA 59.286 34.615 0.00 0.00 37.79 2.52
1944 2434 6.910995 AGATTCTGCATCTCAAAGTTGAAAG 58.089 36.000 0.00 0.00 37.79 2.62
1945 2435 6.889301 AGATTCTGCATCTCAAAGTTGAAA 57.111 33.333 0.00 0.00 37.79 2.69
1946 2436 6.889301 AAGATTCTGCATCTCAAAGTTGAA 57.111 33.333 0.00 0.00 41.93 2.69
1947 2437 7.164122 AGTAAGATTCTGCATCTCAAAGTTGA 58.836 34.615 0.00 0.00 41.93 3.18
1948 2438 7.375106 AGTAAGATTCTGCATCTCAAAGTTG 57.625 36.000 0.00 0.00 41.93 3.16
1949 2439 6.597280 GGAGTAAGATTCTGCATCTCAAAGTT 59.403 38.462 0.00 0.00 41.93 2.66
1950 2440 6.112058 GGAGTAAGATTCTGCATCTCAAAGT 58.888 40.000 0.00 0.00 41.93 2.66
1963 2453 9.860898 ATAAGCAACAAAAATGGAGTAAGATTC 57.139 29.630 0.00 0.00 0.00 2.52
2010 2500 2.159476 CCTGTGATTGTTGAATCGGCTG 60.159 50.000 0.00 0.00 40.96 4.85
2012 2502 1.133025 CCCTGTGATTGTTGAATCGGC 59.867 52.381 0.00 0.00 40.96 5.54
2030 2520 3.509575 TCTTTACAATGGTGCAACATCCC 59.490 43.478 19.55 0.00 39.98 3.85
2033 2523 4.584325 ACACTCTTTACAATGGTGCAACAT 59.416 37.500 12.64 12.64 39.98 2.71
2034 2524 3.951037 ACACTCTTTACAATGGTGCAACA 59.049 39.130 7.04 7.04 39.98 3.33
2054 2544 4.566545 ATTGCGTGAAAGAAATGACACA 57.433 36.364 0.00 0.00 33.56 3.72
2130 2620 3.816523 ACGACCGAGCCAAAGAAATAAAA 59.183 39.130 0.00 0.00 0.00 1.52
2174 2664 8.995220 CAATGTGAGAAACCAAATCATCATTTT 58.005 29.630 0.00 0.00 28.97 1.82
2177 2667 7.235935 ACAATGTGAGAAACCAAATCATCAT 57.764 32.000 0.00 0.00 0.00 2.45
2325 2817 8.783093 CAATAAATGAGAGTGTGTTTGGACTAA 58.217 33.333 0.00 0.00 0.00 2.24
2326 2818 8.154203 TCAATAAATGAGAGTGTGTTTGGACTA 58.846 33.333 0.00 0.00 33.04 2.59
2327 2819 6.998074 TCAATAAATGAGAGTGTGTTTGGACT 59.002 34.615 0.00 0.00 33.04 3.85
2328 2820 7.202016 TCAATAAATGAGAGTGTGTTTGGAC 57.798 36.000 0.00 0.00 33.04 4.02
2329 2821 7.665145 TGATCAATAAATGAGAGTGTGTTTGGA 59.335 33.333 0.00 0.00 42.53 3.53
2330 2822 7.819644 TGATCAATAAATGAGAGTGTGTTTGG 58.180 34.615 0.00 0.00 42.53 3.28
2331 2823 9.850628 AATGATCAATAAATGAGAGTGTGTTTG 57.149 29.630 0.00 0.00 42.53 2.93


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

AutoCloner maintained by Alex Coulton.