Multiple sequence alignment - TraesCS2D01G374900

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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 TraesCS2D01G374900 chr2D 100.000 2673 0 0 1 2673 478701926 478704598 0.000000e+00 4937
1 TraesCS2D01G374900 chr2B 93.817 1876 73 13 802 2673 561230053 561228217 0.000000e+00 2782
2 TraesCS2D01G374900 chr2A 94.826 1063 43 8 808 1859 621482787 621481726 0.000000e+00 1648
3 TraesCS2D01G374900 chr2A 96.649 776 23 2 1898 2673 621481726 621480954 0.000000e+00 1286
4 TraesCS2D01G374900 chr2A 85.241 664 80 15 35 691 621483832 621483180 0.000000e+00 667
5 TraesCS2D01G374900 chr2A 93.750 80 3 1 710 789 621483186 621483109 4.670000e-23 119


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 TraesCS2D01G374900 chr2D 478701926 478704598 2672 False 4937 4937 100.0000 1 2673 1 chr2D.!!$F1 2672
1 TraesCS2D01G374900 chr2B 561228217 561230053 1836 True 2782 2782 93.8170 802 2673 1 chr2B.!!$R1 1871
2 TraesCS2D01G374900 chr2A 621480954 621483832 2878 True 930 1648 92.6165 35 2673 4 chr2A.!!$R1 2638

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
448 452 0.032615 AGCTCCCCTCACGAGAGATT 60.033 55.0 11.76 0.0 44.98 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 2089 0.10412 AAAGCCTTTTTGCCGGTCAC 59.896 50.0 1.9 0.0 0.0 3.67 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
26 27 9.662947 ATCACCACACAATCATATCTATACATG 57.337 33.333 0.00 0.00 0.00 3.21
27 28 8.650490 TCACCACACAATCATATCTATACATGT 58.350 33.333 2.69 2.69 0.00 3.21
28 29 8.715088 CACCACACAATCATATCTATACATGTG 58.285 37.037 9.11 0.00 41.86 3.21
29 30 8.650490 ACCACACAATCATATCTATACATGTGA 58.350 33.333 9.11 0.00 39.30 3.58
30 31 9.148104 CCACACAATCATATCTATACATGTGAG 57.852 37.037 9.11 5.92 39.30 3.51
31 32 8.654215 CACACAATCATATCTATACATGTGAGC 58.346 37.037 9.11 0.00 39.30 4.26
32 33 8.370182 ACACAATCATATCTATACATGTGAGCA 58.630 33.333 9.11 0.00 39.30 4.26
33 34 9.379791 CACAATCATATCTATACATGTGAGCAT 57.620 33.333 9.11 0.00 39.30 3.79
44 45 9.433153 CTATACATGTGAGCATAGAATTGTCAT 57.567 33.333 9.11 0.00 33.30 3.06
46 47 9.955102 ATACATGTGAGCATAGAATTGTCATAT 57.045 29.630 9.11 0.00 33.30 1.78
48 49 9.783081 ACATGTGAGCATAGAATTGTCATATAA 57.217 29.630 0.00 0.00 33.30 0.98
50 51 8.298030 TGTGAGCATAGAATTGTCATATAACG 57.702 34.615 0.00 0.00 0.00 3.18
60 61 2.167487 TGTCATATAACGCAGTGAGCCA 59.833 45.455 0.00 0.00 45.00 4.75
72 75 1.417890 AGTGAGCCAAATATCTCCGGG 59.582 52.381 0.00 0.00 0.00 5.73
84 87 1.760086 CTCCGGGAGCCATCTCACT 60.760 63.158 11.83 0.00 40.62 3.41
93 96 0.731417 GCCATCTCACTCACACATGC 59.269 55.000 0.00 0.00 0.00 4.06
95 98 2.007608 CCATCTCACTCACACATGCTG 58.992 52.381 0.00 0.00 0.00 4.41
97 100 0.668401 TCTCACTCACACATGCTGCG 60.668 55.000 0.00 0.00 0.00 5.18
101 104 0.534877 ACTCACACATGCTGCGGAAA 60.535 50.000 0.00 0.00 0.00 3.13
102 105 0.110056 CTCACACATGCTGCGGAAAC 60.110 55.000 0.00 0.00 0.00 2.78
120 124 0.617820 ACCCTATGGCAGAGGTCGTT 60.618 55.000 25.41 5.31 33.59 3.85
131 135 3.309388 CAGAGGTCGTTAGTGACAACAG 58.691 50.000 0.00 0.00 40.72 3.16
132 136 2.296471 AGAGGTCGTTAGTGACAACAGG 59.704 50.000 0.00 0.00 40.72 4.00
133 137 1.343465 AGGTCGTTAGTGACAACAGGG 59.657 52.381 0.00 0.00 40.72 4.45
144 148 0.680061 ACAACAGGGTCGAGAACTCC 59.320 55.000 0.00 0.00 0.00 3.85
145 149 0.679505 CAACAGGGTCGAGAACTCCA 59.320 55.000 0.00 0.00 0.00 3.86
154 158 3.329542 GAGAACTCCATGGCCGCCA 62.330 63.158 16.17 16.17 38.19 5.69
155 159 3.134127 GAACTCCATGGCCGCCAC 61.134 66.667 16.16 0.00 35.80 5.01
156 160 3.918253 GAACTCCATGGCCGCCACA 62.918 63.158 16.16 0.30 35.80 4.17
157 161 3.286694 AACTCCATGGCCGCCACAT 62.287 57.895 16.16 0.00 35.80 3.21
165 169 3.969802 GCCGCCACATGCCATAGC 61.970 66.667 0.00 0.00 36.24 2.97
166 170 3.289834 CCGCCACATGCCATAGCC 61.290 66.667 0.00 0.00 38.69 3.93
167 171 3.653009 CGCCACATGCCATAGCCG 61.653 66.667 0.00 0.00 38.69 5.52
168 172 2.516930 GCCACATGCCATAGCCGT 60.517 61.111 0.00 0.00 38.69 5.68
169 173 1.227823 GCCACATGCCATAGCCGTA 60.228 57.895 0.00 0.00 38.69 4.02
170 174 1.507141 GCCACATGCCATAGCCGTAC 61.507 60.000 0.00 0.00 38.69 3.67
171 175 0.884704 CCACATGCCATAGCCGTACC 60.885 60.000 0.00 0.00 38.69 3.34
177 181 1.764571 GCCATAGCCGTACCATCCCA 61.765 60.000 0.00 0.00 0.00 4.37
185 189 2.064581 GTACCATCCCAGGGTCGCT 61.065 63.158 5.01 0.00 39.85 4.93
199 203 0.917259 GTCGCTGCTACACATCTTCG 59.083 55.000 0.00 0.00 0.00 3.79
213 217 4.927444 TTCGCGTCGCCGTTGTCA 62.927 61.111 12.44 0.00 36.15 3.58
246 250 1.303888 CTGCCACCATCAACCAGCT 60.304 57.895 0.00 0.00 0.00 4.24
252 256 0.469705 ACCATCAACCAGCTGCCAAA 60.470 50.000 8.66 0.00 0.00 3.28
253 257 0.245539 CCATCAACCAGCTGCCAAAG 59.754 55.000 8.66 0.00 0.00 2.77
254 258 1.250328 CATCAACCAGCTGCCAAAGA 58.750 50.000 8.66 1.54 0.00 2.52
279 283 1.948104 TTGTCGGATTTAGGCATCGG 58.052 50.000 0.00 0.00 0.00 4.18
298 302 1.003118 GGAAGCCCATCACTACACACA 59.997 52.381 0.00 0.00 0.00 3.72
306 310 1.205055 TCACTACACACAACCACCCA 58.795 50.000 0.00 0.00 0.00 4.51
307 311 1.134340 TCACTACACACAACCACCCAC 60.134 52.381 0.00 0.00 0.00 4.61
308 312 0.913205 ACTACACACAACCACCCACA 59.087 50.000 0.00 0.00 0.00 4.17
311 315 2.124487 ACACAACCACCCACACCG 60.124 61.111 0.00 0.00 0.00 4.94
319 323 1.228124 CACCCACACCGTCCATTGT 60.228 57.895 0.00 0.00 0.00 2.71
321 325 0.821711 ACCCACACCGTCCATTGTTG 60.822 55.000 0.00 0.00 0.00 3.33
326 330 1.901464 ACCGTCCATTGTTGCCCAC 60.901 57.895 0.00 0.00 0.00 4.61
366 370 2.752238 CACTCGGAGTCCTCGCCT 60.752 66.667 7.89 0.00 0.00 5.52
369 373 4.091939 TCGGAGTCCTCGCCTCGA 62.092 66.667 7.77 0.00 0.00 4.04
373 377 1.668101 GGAGTCCTCGCCTCGACATT 61.668 60.000 0.41 0.00 0.00 2.71
402 406 3.849953 GACGGTGTCGCGCCATTC 61.850 66.667 0.00 0.00 40.63 2.67
403 407 4.373116 ACGGTGTCGCGCCATTCT 62.373 61.111 0.00 0.00 40.63 2.40
404 408 3.853330 CGGTGTCGCGCCATTCTG 61.853 66.667 0.00 0.00 32.88 3.02
407 411 4.015406 TGTCGCGCCATTCTGGGT 62.015 61.111 0.00 0.00 38.19 4.51
408 412 2.746277 GTCGCGCCATTCTGGGTT 60.746 61.111 0.00 0.00 38.19 4.11
418 422 0.321653 ATTCTGGGTTGTCGTGCCTC 60.322 55.000 0.00 0.00 0.00 4.70
433 437 1.299773 CCTCGCGATTGGAGAGCTC 60.300 63.158 10.36 5.27 40.82 4.09
448 452 0.032615 AGCTCCCCTCACGAGAGATT 60.033 55.000 11.76 0.00 44.98 2.40
449 453 0.387565 GCTCCCCTCACGAGAGATTC 59.612 60.000 11.76 0.00 44.98 2.52
450 454 1.769026 CTCCCCTCACGAGAGATTCA 58.231 55.000 11.76 0.00 44.98 2.57
456 460 0.109272 TCACGAGAGATTCACCGCAC 60.109 55.000 0.00 0.00 0.00 5.34
467 471 1.153647 CACCGCACGAGAAGGCATA 60.154 57.895 0.00 0.00 0.00 3.14
479 483 3.227250 GGCATACCTACCAGCGGT 58.773 61.111 5.58 5.58 40.16 5.68
496 500 1.610673 GTGACAGCTGGGGGAGAGA 60.611 63.158 19.93 0.00 0.00 3.10
504 508 0.041833 CTGGGGGAGAGAAGGAGACA 59.958 60.000 0.00 0.00 0.00 3.41
515 519 2.143925 GAAGGAGACAACCAGGTTTCG 58.856 52.381 0.44 0.00 0.00 3.46
526 530 1.079127 AGGTTTCGTGGGAGATGCG 60.079 57.895 0.00 0.00 0.00 4.73
559 563 5.968676 TGTTTCCCTAGGTTGCATACTAT 57.031 39.130 8.29 0.00 0.00 2.12
629 636 5.279859 GGAGATGCTCTGATGGAATATGACA 60.280 44.000 0.00 0.00 0.00 3.58
631 638 3.721035 TGCTCTGATGGAATATGACACG 58.279 45.455 0.00 0.00 0.00 4.49
633 640 2.728318 CTCTGATGGAATATGACACGCG 59.272 50.000 3.53 3.53 0.00 6.01
641 648 4.336153 TGGAATATGACACGCGTTCTAGTA 59.664 41.667 10.22 0.00 0.00 1.82
648 655 3.870007 ACACGCGTTCTAGTATGTATCG 58.130 45.455 10.22 0.00 0.00 2.92
660 667 8.707796 TCTAGTATGTATCGGAGGAAAAGAAT 57.292 34.615 0.00 0.00 0.00 2.40
665 672 3.567478 ATCGGAGGAAAAGAATGGGAG 57.433 47.619 0.00 0.00 0.00 4.30
667 674 1.340017 CGGAGGAAAAGAATGGGAGCA 60.340 52.381 0.00 0.00 0.00 4.26
671 678 3.766051 GAGGAAAAGAATGGGAGCAACAT 59.234 43.478 0.00 0.00 0.00 2.71
675 682 0.911769 AGAATGGGAGCAACATCGGA 59.088 50.000 0.00 0.00 0.00 4.55
681 688 1.401905 GGGAGCAACATCGGACAATTC 59.598 52.381 0.00 0.00 0.00 2.17
685 692 3.614092 AGCAACATCGGACAATTCATCT 58.386 40.909 0.00 0.00 0.00 2.90
691 698 6.824305 ACATCGGACAATTCATCTTCTTTT 57.176 33.333 0.00 0.00 0.00 2.27
713 720 6.469782 TTTTCTTTGAAACAATGAGCCTCT 57.530 33.333 0.00 0.00 0.00 3.69
714 721 6.469782 TTTCTTTGAAACAATGAGCCTCTT 57.530 33.333 0.00 0.00 0.00 2.85
715 722 6.469782 TTCTTTGAAACAATGAGCCTCTTT 57.530 33.333 0.00 0.00 0.00 2.52
716 723 5.835257 TCTTTGAAACAATGAGCCTCTTTG 58.165 37.500 16.36 16.36 37.49 2.77
717 724 5.360714 TCTTTGAAACAATGAGCCTCTTTGT 59.639 36.000 17.52 17.52 43.68 2.83
718 725 4.836125 TGAAACAATGAGCCTCTTTGTC 57.164 40.909 21.85 13.33 41.84 3.18
719 726 3.250762 TGAAACAATGAGCCTCTTTGTCG 59.749 43.478 21.85 1.51 41.84 4.35
720 727 2.839486 ACAATGAGCCTCTTTGTCGA 57.161 45.000 17.52 0.00 39.57 4.20
721 728 3.340814 ACAATGAGCCTCTTTGTCGAT 57.659 42.857 17.52 0.00 39.57 3.59
722 729 3.679389 ACAATGAGCCTCTTTGTCGATT 58.321 40.909 17.52 0.00 39.57 3.34
737 744 9.458374 TCTTTGTCGATTTTCATTAAAGAAACC 57.542 29.630 5.40 1.20 37.24 3.27
738 745 9.243637 CTTTGTCGATTTTCATTAAAGAAACCA 57.756 29.630 5.40 0.00 37.24 3.67
779 786 5.243060 AGGTTATAGCAAAACAGGGAAACAC 59.757 40.000 0.00 0.00 0.00 3.32
790 797 2.351706 GGGAAACACACCCAACTACA 57.648 50.000 0.00 0.00 46.05 2.74
791 798 2.657143 GGGAAACACACCCAACTACAA 58.343 47.619 0.00 0.00 46.05 2.41
793 800 3.284617 GGAAACACACCCAACTACAAGT 58.715 45.455 0.00 0.00 0.00 3.16
794 801 3.066203 GGAAACACACCCAACTACAAGTG 59.934 47.826 0.00 0.00 36.30 3.16
795 802 3.637911 AACACACCCAACTACAAGTGA 57.362 42.857 0.00 0.00 34.33 3.41
796 803 3.637911 ACACACCCAACTACAAGTGAA 57.362 42.857 0.00 0.00 34.33 3.18
797 804 3.275999 ACACACCCAACTACAAGTGAAC 58.724 45.455 0.00 0.00 34.33 3.18
798 805 3.275143 CACACCCAACTACAAGTGAACA 58.725 45.455 0.00 0.00 34.33 3.18
799 806 3.692101 CACACCCAACTACAAGTGAACAA 59.308 43.478 0.00 0.00 34.33 2.83
800 807 3.692593 ACACCCAACTACAAGTGAACAAC 59.307 43.478 0.00 0.00 34.33 3.32
818 1128 3.181476 ACAACAAACCAGCAATTCAGTCC 60.181 43.478 0.00 0.00 0.00 3.85
1122 1433 2.113139 CAGGAACCAACCGGCAGT 59.887 61.111 0.00 0.00 34.57 4.40
1481 1798 1.787155 CGACCTCTTCAACAACGTCAG 59.213 52.381 0.00 0.00 0.00 3.51
1503 1820 0.535335 GAGTAGGGGATCGCACACAA 59.465 55.000 12.32 0.00 0.00 3.33
1511 1828 2.223572 GGGATCGCACACAAATCAATCC 60.224 50.000 4.64 0.00 0.00 3.01
1528 1845 2.042831 CCGCCTTTTGAGCCTCTGG 61.043 63.158 0.00 0.00 0.00 3.86
1716 2033 1.153132 AGGATAGAGGGGGAGATTGGG 59.847 57.143 0.00 0.00 0.00 4.12
1723 2043 1.644337 AGGGGGAGATTGGGTAAAACC 59.356 52.381 0.00 0.00 37.60 3.27
1758 2078 5.856126 TTACGTTTGCATACAAGGAGAAG 57.144 39.130 8.06 0.00 37.04 2.85
1764 2084 5.726980 TTGCATACAAGGAGAAGCAAATT 57.273 34.783 0.00 0.00 38.82 1.82
1769 2089 8.623903 TGCATACAAGGAGAAGCAAATTAATAG 58.376 33.333 0.00 0.00 0.00 1.73
1770 2090 8.624776 GCATACAAGGAGAAGCAAATTAATAGT 58.375 33.333 0.00 0.00 0.00 2.12
1786 2106 0.109723 TAGTGACCGGCAAAAAGGCT 59.890 50.000 0.00 0.00 41.46 4.58
1835 2155 9.719355 TCTTATTATCTTCTTGTTGTTGCTACA 57.281 29.630 0.00 0.00 0.00 2.74
1838 2158 8.798859 ATTATCTTCTTGTTGTTGCTACATCT 57.201 30.769 0.81 0.00 33.44 2.90
1839 2159 8.621532 TTATCTTCTTGTTGTTGCTACATCTT 57.378 30.769 0.81 0.00 33.44 2.40
1840 2160 6.545504 TCTTCTTGTTGTTGCTACATCTTC 57.454 37.500 0.81 0.00 33.44 2.87
1841 2161 6.291377 TCTTCTTGTTGTTGCTACATCTTCT 58.709 36.000 0.81 0.00 33.44 2.85
1842 2162 7.441836 TCTTCTTGTTGTTGCTACATCTTCTA 58.558 34.615 0.81 0.00 33.44 2.10
1843 2163 7.385205 TCTTCTTGTTGTTGCTACATCTTCTAC 59.615 37.037 0.81 0.00 33.44 2.59
1844 2164 6.759272 TCTTGTTGTTGCTACATCTTCTACT 58.241 36.000 0.81 0.00 33.44 2.57
1845 2165 7.892609 TCTTGTTGTTGCTACATCTTCTACTA 58.107 34.615 0.81 0.00 33.44 1.82
1846 2166 8.364894 TCTTGTTGTTGCTACATCTTCTACTAA 58.635 33.333 0.81 0.00 33.44 2.24
2080 2423 1.337071 TGACTCTATTCGTCGCCATCC 59.663 52.381 0.00 0.00 34.17 3.51
2121 2464 9.080097 AGCAGTATTTATCTTCCTATAACTCGT 57.920 33.333 0.00 0.00 0.00 4.18
2150 2493 4.759782 ACCGATGAAGTTTCAGTATCTGG 58.240 43.478 0.74 3.23 41.08 3.86
2316 2659 2.095567 CGAACTCCAAAGCAGTTCATGG 60.096 50.000 12.69 0.19 46.99 3.66
2368 2711 5.530915 CAGAACCTCAAACTGGTTTGTGATA 59.469 40.000 21.90 7.25 46.59 2.15
2407 2750 4.384056 AGTGACATCAACTGGAAGAACTG 58.616 43.478 0.00 0.00 37.43 3.16
2548 2891 8.186709 CATCATTAGAGGCAGGGATTTATTTT 57.813 34.615 0.00 0.00 0.00 1.82
2549 2892 8.645110 CATCATTAGAGGCAGGGATTTATTTTT 58.355 33.333 0.00 0.00 0.00 1.94
2670 3013 1.132453 TCACGCGATTGAAGAGATCGT 59.868 47.619 15.93 0.00 45.99 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.662947 CATGTATAGATATGATTGTGTGGTGAT 57.337 33.333 0.00 0.00 0.00 3.06
1 2 8.650490 ACATGTATAGATATGATTGTGTGGTGA 58.350 33.333 0.00 0.00 0.00 4.02
2 3 8.715088 CACATGTATAGATATGATTGTGTGGTG 58.285 37.037 0.00 0.00 32.03 4.17
3 4 8.650490 TCACATGTATAGATATGATTGTGTGGT 58.350 33.333 0.00 0.00 35.79 4.16
4 5 9.148104 CTCACATGTATAGATATGATTGTGTGG 57.852 37.037 0.00 0.00 35.79 4.17
5 6 8.654215 GCTCACATGTATAGATATGATTGTGTG 58.346 37.037 10.74 0.00 35.79 3.82
6 7 8.370182 TGCTCACATGTATAGATATGATTGTGT 58.630 33.333 10.74 0.00 35.79 3.72
7 8 8.767478 TGCTCACATGTATAGATATGATTGTG 57.233 34.615 10.74 0.00 35.67 3.33
16 17 9.650539 GACAATTCTATGCTCACATGTATAGAT 57.349 33.333 14.09 3.10 39.88 1.98
17 18 8.641541 TGACAATTCTATGCTCACATGTATAGA 58.358 33.333 10.67 10.67 38.97 1.98
18 19 8.822652 TGACAATTCTATGCTCACATGTATAG 57.177 34.615 0.00 2.38 37.04 1.31
20 21 9.955102 ATATGACAATTCTATGCTCACATGTAT 57.045 29.630 0.00 0.00 37.04 2.29
22 23 9.783081 TTATATGACAATTCTATGCTCACATGT 57.217 29.630 0.00 0.00 37.04 3.21
24 25 8.929746 CGTTATATGACAATTCTATGCTCACAT 58.070 33.333 0.00 0.00 40.49 3.21
25 26 7.095649 GCGTTATATGACAATTCTATGCTCACA 60.096 37.037 0.00 0.00 0.00 3.58
26 27 7.095649 TGCGTTATATGACAATTCTATGCTCAC 60.096 37.037 0.00 0.00 0.00 3.51
27 28 6.928492 TGCGTTATATGACAATTCTATGCTCA 59.072 34.615 0.00 0.00 0.00 4.26
28 29 7.116948 ACTGCGTTATATGACAATTCTATGCTC 59.883 37.037 0.00 0.00 0.00 4.26
29 30 6.931281 ACTGCGTTATATGACAATTCTATGCT 59.069 34.615 0.00 0.00 0.00 3.79
30 31 7.011773 CACTGCGTTATATGACAATTCTATGC 58.988 38.462 0.00 0.00 0.00 3.14
31 32 8.298030 TCACTGCGTTATATGACAATTCTATG 57.702 34.615 0.00 0.00 0.00 2.23
32 33 7.116948 GCTCACTGCGTTATATGACAATTCTAT 59.883 37.037 0.00 0.00 0.00 1.98
33 34 6.420903 GCTCACTGCGTTATATGACAATTCTA 59.579 38.462 0.00 0.00 0.00 2.10
44 45 5.853936 AGATATTTGGCTCACTGCGTTATA 58.146 37.500 0.00 0.00 44.05 0.98
45 46 4.708177 AGATATTTGGCTCACTGCGTTAT 58.292 39.130 0.00 0.00 44.05 1.89
46 47 4.119862 GAGATATTTGGCTCACTGCGTTA 58.880 43.478 0.00 0.00 44.05 3.18
48 49 2.555199 GAGATATTTGGCTCACTGCGT 58.445 47.619 0.00 0.00 44.05 5.24
50 51 1.869767 CGGAGATATTTGGCTCACTGC 59.130 52.381 0.00 0.00 41.94 4.40
54 55 1.694150 CTCCCGGAGATATTTGGCTCA 59.306 52.381 9.01 0.00 32.83 4.26
60 61 2.569404 GAGATGGCTCCCGGAGATATTT 59.431 50.000 19.33 6.38 35.01 1.40
72 75 2.277969 CATGTGTGAGTGAGATGGCTC 58.722 52.381 0.00 0.00 41.67 4.70
93 96 1.077787 TGCCATAGGGTTTCCGCAG 60.078 57.895 0.00 0.00 38.33 5.18
95 98 0.815615 CTCTGCCATAGGGTTTCCGC 60.816 60.000 0.00 0.00 38.33 5.54
97 100 0.919710 ACCTCTGCCATAGGGTTTCC 59.080 55.000 0.81 0.00 38.54 3.13
101 104 0.617820 AACGACCTCTGCCATAGGGT 60.618 55.000 0.81 0.00 38.54 4.34
102 105 1.341531 CTAACGACCTCTGCCATAGGG 59.658 57.143 0.81 0.00 38.54 3.53
120 124 2.281539 TCTCGACCCTGTTGTCACTA 57.718 50.000 0.00 0.00 34.88 2.74
131 135 1.153349 GCCATGGAGTTCTCGACCC 60.153 63.158 18.40 0.00 0.00 4.46
132 136 1.153349 GGCCATGGAGTTCTCGACC 60.153 63.158 18.40 0.00 0.00 4.79
133 137 1.519455 CGGCCATGGAGTTCTCGAC 60.519 63.158 18.40 0.00 0.00 4.20
154 158 0.764890 ATGGTACGGCTATGGCATGT 59.235 50.000 10.98 3.29 40.87 3.21
155 159 1.442769 GATGGTACGGCTATGGCATG 58.557 55.000 10.98 1.26 40.87 4.06
156 160 0.324943 GGATGGTACGGCTATGGCAT 59.675 55.000 4.88 4.88 40.87 4.40
157 161 1.752198 GGATGGTACGGCTATGGCA 59.248 57.895 2.58 0.00 40.87 4.92
160 164 0.321671 CCTGGGATGGTACGGCTATG 59.678 60.000 0.00 0.00 0.00 2.23
162 166 1.458777 CCCTGGGATGGTACGGCTA 60.459 63.158 7.01 0.00 0.00 3.93
164 168 3.087906 ACCCTGGGATGGTACGGC 61.088 66.667 22.23 0.00 33.26 5.68
165 169 2.792947 CGACCCTGGGATGGTACGG 61.793 68.421 22.23 0.00 35.85 4.02
166 170 2.812499 CGACCCTGGGATGGTACG 59.188 66.667 22.23 10.68 35.85 3.67
167 171 2.064581 AGCGACCCTGGGATGGTAC 61.065 63.158 22.23 2.29 35.85 3.34
168 172 2.063979 CAGCGACCCTGGGATGGTA 61.064 63.158 22.23 0.00 37.93 3.25
169 173 3.402681 CAGCGACCCTGGGATGGT 61.403 66.667 22.23 13.67 37.93 3.55
170 174 4.864334 GCAGCGACCCTGGGATGG 62.864 72.222 22.23 8.89 42.03 3.51
171 175 2.434843 TAGCAGCGACCCTGGGATG 61.435 63.158 22.23 12.19 42.03 3.51
177 181 0.972983 AGATGTGTAGCAGCGACCCT 60.973 55.000 2.88 0.00 38.76 4.34
185 189 0.796870 CGACGCGAAGATGTGTAGCA 60.797 55.000 15.93 0.00 31.57 3.49
225 229 1.228521 TGGTTGATGGTGGCAGTGG 60.229 57.895 0.00 0.00 0.00 4.00
227 231 1.604593 GCTGGTTGATGGTGGCAGT 60.605 57.895 0.00 0.00 0.00 4.40
236 240 1.251251 GTCTTTGGCAGCTGGTTGAT 58.749 50.000 17.12 0.00 0.00 2.57
254 258 2.290641 TGCCTAAATCCGACAATGGTGT 60.291 45.455 0.00 0.00 42.10 4.16
265 269 1.239347 GGCTTCCGATGCCTAAATCC 58.761 55.000 16.31 0.00 46.38 3.01
279 283 2.472695 TGTGTGTAGTGATGGGCTTC 57.527 50.000 0.00 0.00 0.00 3.86
298 302 2.002018 AATGGACGGTGTGGGTGGTT 62.002 55.000 0.00 0.00 0.00 3.67
306 310 1.901464 GGGCAACAATGGACGGTGT 60.901 57.895 0.00 0.00 39.74 4.16
307 311 1.900981 TGGGCAACAATGGACGGTG 60.901 57.895 0.00 0.00 39.74 4.94
308 312 1.901464 GTGGGCAACAATGGACGGT 60.901 57.895 0.00 0.00 39.74 4.83
311 315 2.258286 GCGTGGGCAACAATGGAC 59.742 61.111 0.00 0.00 39.62 4.02
366 370 1.408702 TCGATGGAGCATGAATGTCGA 59.591 47.619 0.00 1.64 34.69 4.20
369 373 1.575244 CGTCGATGGAGCATGAATGT 58.425 50.000 0.00 0.00 0.00 2.71
373 377 1.141665 CACCGTCGATGGAGCATGA 59.858 57.895 30.28 0.00 0.00 3.07
402 406 2.738521 CGAGGCACGACAACCCAG 60.739 66.667 0.00 0.00 45.77 4.45
403 407 4.980805 GCGAGGCACGACAACCCA 62.981 66.667 8.92 0.00 45.77 4.51
407 411 2.048597 AATCGCGAGGCACGACAA 60.049 55.556 16.66 0.00 43.23 3.18
408 412 2.809174 CAATCGCGAGGCACGACA 60.809 61.111 16.66 0.00 43.23 4.35
433 437 0.461961 GGTGAATCTCTCGTGAGGGG 59.538 60.000 14.12 0.00 40.58 4.79
436 440 0.171231 TGCGGTGAATCTCTCGTGAG 59.829 55.000 8.20 8.20 41.51 3.51
439 443 1.154016 CGTGCGGTGAATCTCTCGT 60.154 57.895 0.00 0.00 0.00 4.18
448 452 1.600511 TATGCCTTCTCGTGCGGTGA 61.601 55.000 0.00 0.00 0.00 4.02
449 453 1.153647 TATGCCTTCTCGTGCGGTG 60.154 57.895 0.00 0.00 0.00 4.94
450 454 1.153628 GTATGCCTTCTCGTGCGGT 60.154 57.895 0.00 0.00 0.00 5.68
456 460 1.269831 GCTGGTAGGTATGCCTTCTCG 60.270 57.143 7.98 0.00 44.18 4.04
467 471 2.943978 GCTGTCACCGCTGGTAGGT 61.944 63.158 0.00 0.00 43.97 3.08
479 483 0.906756 CTTCTCTCCCCCAGCTGTCA 60.907 60.000 13.81 0.00 0.00 3.58
488 492 0.906066 GGTTGTCTCCTTCTCTCCCC 59.094 60.000 0.00 0.00 0.00 4.81
496 500 1.489230 ACGAAACCTGGTTGTCTCCTT 59.511 47.619 13.79 0.00 0.00 3.36
504 508 1.064825 ATCTCCCACGAAACCTGGTT 58.935 50.000 6.18 6.18 0.00 3.67
515 519 0.533755 CCATCTTCCGCATCTCCCAC 60.534 60.000 0.00 0.00 0.00 4.61
580 584 7.968405 CCGGATGGTCTAATTGTTCTTTTTAAG 59.032 37.037 0.00 0.00 0.00 1.85
583 587 6.007703 TCCGGATGGTCTAATTGTTCTTTTT 58.992 36.000 0.00 0.00 36.30 1.94
584 588 5.566469 TCCGGATGGTCTAATTGTTCTTTT 58.434 37.500 0.00 0.00 36.30 2.27
585 589 5.045869 TCTCCGGATGGTCTAATTGTTCTTT 60.046 40.000 3.57 0.00 36.30 2.52
614 621 2.473816 ACGCGTGTCATATTCCATCAG 58.526 47.619 12.93 0.00 0.00 2.90
629 636 3.133691 TCCGATACATACTAGAACGCGT 58.866 45.455 5.58 5.58 0.00 6.01
631 638 3.750130 TCCTCCGATACATACTAGAACGC 59.250 47.826 0.00 0.00 0.00 4.84
633 640 7.938715 TCTTTTCCTCCGATACATACTAGAAC 58.061 38.462 0.00 0.00 0.00 3.01
641 648 4.412199 TCCCATTCTTTTCCTCCGATACAT 59.588 41.667 0.00 0.00 0.00 2.29
648 655 2.493675 GTTGCTCCCATTCTTTTCCTCC 59.506 50.000 0.00 0.00 0.00 4.30
660 667 0.327924 ATTGTCCGATGTTGCTCCCA 59.672 50.000 0.00 0.00 0.00 4.37
665 672 4.095483 AGAAGATGAATTGTCCGATGTTGC 59.905 41.667 0.00 0.00 0.00 4.17
667 674 6.824305 AAAGAAGATGAATTGTCCGATGTT 57.176 33.333 0.00 0.00 0.00 2.71
691 698 6.469782 AAGAGGCTCATTGTTTCAAAGAAA 57.530 33.333 18.26 0.00 0.00 2.52
693 700 5.360714 ACAAAGAGGCTCATTGTTTCAAAGA 59.639 36.000 27.21 0.00 35.07 2.52
694 701 5.594926 ACAAAGAGGCTCATTGTTTCAAAG 58.405 37.500 27.21 6.48 35.07 2.77
695 702 5.591099 GACAAAGAGGCTCATTGTTTCAAA 58.409 37.500 31.39 0.00 38.26 2.69
696 703 4.261155 CGACAAAGAGGCTCATTGTTTCAA 60.261 41.667 31.39 0.00 38.26 2.69
697 704 3.250762 CGACAAAGAGGCTCATTGTTTCA 59.749 43.478 31.39 0.00 38.26 2.69
698 705 3.498397 TCGACAAAGAGGCTCATTGTTTC 59.502 43.478 31.39 21.30 38.26 2.78
699 706 3.476552 TCGACAAAGAGGCTCATTGTTT 58.523 40.909 31.39 15.55 38.26 2.83
700 707 3.126001 TCGACAAAGAGGCTCATTGTT 57.874 42.857 31.39 19.06 38.26 2.83
701 708 2.839486 TCGACAAAGAGGCTCATTGT 57.161 45.000 31.37 31.37 40.47 2.71
702 709 4.691860 AAATCGACAAAGAGGCTCATTG 57.308 40.909 25.99 25.99 31.97 2.82
703 710 4.761739 TGAAAATCGACAAAGAGGCTCATT 59.238 37.500 18.26 8.43 0.00 2.57
704 711 4.326826 TGAAAATCGACAAAGAGGCTCAT 58.673 39.130 18.26 0.57 0.00 2.90
705 712 3.738982 TGAAAATCGACAAAGAGGCTCA 58.261 40.909 18.26 0.00 0.00 4.26
706 713 4.954092 ATGAAAATCGACAAAGAGGCTC 57.046 40.909 6.34 6.34 0.00 4.70
707 714 6.817765 TTAATGAAAATCGACAAAGAGGCT 57.182 33.333 0.00 0.00 0.00 4.58
708 715 7.305474 TCTTTAATGAAAATCGACAAAGAGGC 58.695 34.615 0.00 0.00 0.00 4.70
709 716 9.677567 TTTCTTTAATGAAAATCGACAAAGAGG 57.322 29.630 12.68 0.00 33.50 3.69
711 718 9.458374 GGTTTCTTTAATGAAAATCGACAAAGA 57.542 29.630 15.76 0.00 37.63 2.52
712 719 9.243637 TGGTTTCTTTAATGAAAATCGACAAAG 57.756 29.630 15.76 0.00 37.63 2.77
713 720 9.026074 GTGGTTTCTTTAATGAAAATCGACAAA 57.974 29.630 15.76 0.00 37.63 2.83
714 721 7.650104 GGTGGTTTCTTTAATGAAAATCGACAA 59.350 33.333 15.76 0.00 37.63 3.18
715 722 7.142680 GGTGGTTTCTTTAATGAAAATCGACA 58.857 34.615 15.76 9.04 37.63 4.35
716 723 7.142680 TGGTGGTTTCTTTAATGAAAATCGAC 58.857 34.615 15.76 12.01 37.63 4.20
717 724 7.278461 TGGTGGTTTCTTTAATGAAAATCGA 57.722 32.000 15.76 0.00 37.63 3.59
718 725 7.812191 TGATGGTGGTTTCTTTAATGAAAATCG 59.188 33.333 15.76 0.00 37.63 3.34
719 726 9.487790 TTGATGGTGGTTTCTTTAATGAAAATC 57.512 29.630 15.76 14.40 37.63 2.17
720 727 9.492973 CTTGATGGTGGTTTCTTTAATGAAAAT 57.507 29.630 15.76 7.57 37.63 1.82
721 728 8.482128 ACTTGATGGTGGTTTCTTTAATGAAAA 58.518 29.630 15.76 3.63 37.63 2.29
722 729 8.017418 ACTTGATGGTGGTTTCTTTAATGAAA 57.983 30.769 11.39 11.39 34.05 2.69
737 744 9.840427 CTATAACCTTTGTAAAACTTGATGGTG 57.160 33.333 0.00 0.00 0.00 4.17
738 745 8.520351 GCTATAACCTTTGTAAAACTTGATGGT 58.480 33.333 0.00 0.00 0.00 3.55
779 786 3.692101 TGTTGTTCACTTGTAGTTGGGTG 59.308 43.478 0.00 0.00 0.00 4.61
789 796 3.229276 TGCTGGTTTGTTGTTCACTTG 57.771 42.857 0.00 0.00 0.00 3.16
790 797 3.951775 TTGCTGGTTTGTTGTTCACTT 57.048 38.095 0.00 0.00 0.00 3.16
791 798 4.081752 TGAATTGCTGGTTTGTTGTTCACT 60.082 37.500 0.00 0.00 0.00 3.41
793 800 4.081752 ACTGAATTGCTGGTTTGTTGTTCA 60.082 37.500 0.00 0.00 0.00 3.18
794 801 4.432712 ACTGAATTGCTGGTTTGTTGTTC 58.567 39.130 0.00 0.00 0.00 3.18
795 802 4.432712 GACTGAATTGCTGGTTTGTTGTT 58.567 39.130 0.00 0.00 0.00 2.83
796 803 3.181476 GGACTGAATTGCTGGTTTGTTGT 60.181 43.478 0.00 0.00 0.00 3.32
797 804 3.181477 TGGACTGAATTGCTGGTTTGTTG 60.181 43.478 0.00 0.00 0.00 3.33
798 805 3.030291 TGGACTGAATTGCTGGTTTGTT 58.970 40.909 0.00 0.00 0.00 2.83
799 806 2.665165 TGGACTGAATTGCTGGTTTGT 58.335 42.857 0.00 0.00 0.00 2.83
800 807 3.731652 TTGGACTGAATTGCTGGTTTG 57.268 42.857 0.00 0.00 0.00 2.93
1481 1798 1.068250 GTGCGATCCCCTACTCTGC 59.932 63.158 0.00 0.00 0.00 4.26
1503 1820 1.478105 GGCTCAAAAGGCGGATTGATT 59.522 47.619 3.73 0.00 38.44 2.57
1707 2024 4.028993 TGTCTGGTTTTACCCAATCTCC 57.971 45.455 0.00 0.00 37.50 3.71
1723 2043 3.485216 GCAAACGTAAATCCGGATGTCTG 60.485 47.826 19.95 9.63 0.00 3.51
1758 2078 4.364415 TTGCCGGTCACTATTAATTTGC 57.636 40.909 1.90 0.00 0.00 3.68
1764 2084 2.750712 GCCTTTTTGCCGGTCACTATTA 59.249 45.455 1.90 0.00 0.00 0.98
1769 2089 0.104120 AAAGCCTTTTTGCCGGTCAC 59.896 50.000 1.90 0.00 0.00 3.67
1770 2090 0.827368 AAAAGCCTTTTTGCCGGTCA 59.173 45.000 1.90 0.00 35.26 4.02
1817 2137 6.291377 AGAAGATGTAGCAACAACAAGAAGA 58.709 36.000 0.00 0.00 39.58 2.87
1842 2162 9.802039 CCTCCAGAGAGTAGAGTAAATATTAGT 57.198 37.037 0.00 0.00 38.58 2.24
1845 2165 8.934023 CTCCTCCAGAGAGTAGAGTAAATATT 57.066 38.462 0.00 0.00 46.50 1.28
2080 2423 2.703409 GCTTCAGCATGTACGCCG 59.297 61.111 0.00 0.00 41.59 6.46
2121 2464 4.022589 ACTGAAACTTCATCGGTAGTTCGA 60.023 41.667 0.00 0.00 43.61 3.71
2380 2723 6.911250 TCTTCCAGTTGATGTCACTACTTA 57.089 37.500 0.00 0.00 0.00 2.24
2407 2750 3.118261 TGCTCCCAGATCTTACAATGGTC 60.118 47.826 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.