Multiple sequence alignment - TraesCS2A01G495300

Loading Multiple Alignment...

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 TraesCS2A01G495300 chr2A 100.000 2354 0 0 1 2354 726955398 726953045 0.000000e+00 4348.0
1 TraesCS2A01G495300 chr2A 81.592 201 34 2 132 332 733451269 733451072 1.870000e-36 163.0
2 TraesCS2A01G495300 chr2A 87.671 73 8 1 1522 1594 726953522 726953451 1.500000e-12 84.2
3 TraesCS2A01G495300 chr2A 87.671 73 8 1 1877 1948 726953877 726953805 1.500000e-12 84.2
4 TraesCS2A01G495300 chr2D 89.583 912 47 23 823 1722 592376655 592375780 0.000000e+00 1114.0
5 TraesCS2A01G495300 chr2D 92.048 503 28 5 13 510 592397656 592397161 0.000000e+00 697.0
6 TraesCS2A01G495300 chr2D 90.741 432 32 6 1877 2302 592375776 592375347 9.440000e-159 569.0
7 TraesCS2A01G495300 chr2D 80.712 337 53 6 11 346 448193481 448193156 3.880000e-63 252.0
8 TraesCS2A01G495300 chr2D 96.575 146 4 1 625 770 592396761 592396617 8.410000e-60 241.0
9 TraesCS2A01G495300 chr2D 87.730 163 10 6 473 626 592397161 592397000 5.170000e-42 182.0
10 TraesCS2A01G495300 chr2D 96.296 54 2 0 2301 2354 592375314 592375261 3.220000e-14 89.8
11 TraesCS2A01G495300 chr2B 90.041 723 44 14 620 1338 718215157 718214459 0.000000e+00 911.0
12 TraesCS2A01G495300 chr2B 88.865 467 46 2 1 467 718217459 718216999 9.440000e-159 569.0
13 TraesCS2A01G495300 chr2B 87.059 340 26 11 1387 1722 718214450 718214125 3.700000e-98 368.0
14 TraesCS2A01G495300 chr2B 76.218 349 68 9 2 348 569267454 569267789 1.120000e-38 171.0
15 TraesCS2A01G495300 chr3B 75.811 339 53 19 1 338 19412832 19413142 6.780000e-31 145.0
16 TraesCS2A01G495300 chr1D 81.132 106 14 6 1772 1876 42974455 42974555 1.940000e-11 80.5


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 TraesCS2A01G495300 chr2A 726953045 726955398 2353 True 1505.466667 4348 91.780667 1 2354 3 chr2A.!!$R2 2353
1 TraesCS2A01G495300 chr2D 592375261 592376655 1394 True 590.933333 1114 92.206667 823 2354 3 chr2D.!!$R2 1531
2 TraesCS2A01G495300 chr2D 592396617 592397656 1039 True 373.333333 697 92.117667 13 770 3 chr2D.!!$R3 757
3 TraesCS2A01G495300 chr2B 718214125 718217459 3334 True 616.000000 911 88.655000 1 1722 3 chr2B.!!$R1 1721

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
546 851 0.026674 TACGACGCGTCCAGTAATCG 59.973 55.0 31.84 20.84 41.54 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1362 3307 0.45826 TAACAGCATAGCGGCGAAGA 59.542 50.0 12.98 0.0 39.27 2.87 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
53 54 2.737180 CGGTGCTCTGGTGTGAGT 59.263 61.111 0.00 0.00 36.51 3.41
79 80 6.200878 AGAATAGGTGGTCTTCTTTTGGAA 57.799 37.500 0.00 0.00 0.00 3.53
152 153 0.846693 GAGGTGGTGGATATGGGCTT 59.153 55.000 0.00 0.00 0.00 4.35
189 190 0.417841 AGGTAGGAGGTGGATGTGGT 59.582 55.000 0.00 0.00 0.00 4.16
191 192 1.633945 GGTAGGAGGTGGATGTGGTTT 59.366 52.381 0.00 0.00 0.00 3.27
199 200 0.470833 TGGATGTGGTTTGGGTTGGG 60.471 55.000 0.00 0.00 0.00 4.12
223 224 1.284785 TGCTGGCTGGGTTAAATAGCT 59.715 47.619 0.00 0.00 37.58 3.32
274 275 2.029073 CCACGAGGCGTTCACACT 59.971 61.111 0.00 0.00 38.32 3.55
333 334 0.320374 GGACGATTCTGTGTGGGACA 59.680 55.000 0.00 0.00 0.00 4.02
504 572 0.869730 TGCGATGCAATGATGATCCG 59.130 50.000 0.00 0.00 34.76 4.18
529 834 8.108172 CGGCGTATTGATCATGTTTATACATAC 58.892 37.037 12.65 6.76 43.07 2.39
546 851 0.026674 TACGACGCGTCCAGTAATCG 59.973 55.000 31.84 20.84 41.54 3.34
549 854 1.343506 GACGCGTCCAGTAATCGTTT 58.656 50.000 28.61 0.00 33.21 3.60
550 855 1.058695 GACGCGTCCAGTAATCGTTTG 59.941 52.381 28.61 0.00 33.21 2.93
555 904 2.629051 GTCCAGTAATCGTTTGAGGGG 58.371 52.381 0.00 0.00 0.00 4.79
590 939 4.389077 GTGGCTGTAGATGTTGTAAGTGAC 59.611 45.833 0.00 0.00 0.00 3.67
645 2575 0.321919 TAAGCAGTGGCAGGCTCTTG 60.322 55.000 13.32 0.00 44.61 3.02
721 2651 3.381949 GGACATTATTAGCTTCGCTCGT 58.618 45.455 0.00 0.00 40.44 4.18
736 2666 0.807667 CTCGTAAGGCTCGCTGCAAT 60.808 55.000 0.00 0.00 45.15 3.56
797 2727 1.337354 TGCGCGGTAATCTTTGACTCA 60.337 47.619 8.83 0.00 0.00 3.41
830 2761 6.644347 TCTTCAGTCTTCACCATTTATCTCC 58.356 40.000 0.00 0.00 0.00 3.71
875 2806 4.074970 CAAGCACAACCATTTACTCCTCT 58.925 43.478 0.00 0.00 0.00 3.69
877 2808 3.327757 AGCACAACCATTTACTCCTCTGA 59.672 43.478 0.00 0.00 0.00 3.27
879 2810 4.702131 GCACAACCATTTACTCCTCTGAAT 59.298 41.667 0.00 0.00 0.00 2.57
883 2814 7.607991 CACAACCATTTACTCCTCTGAATTACT 59.392 37.037 0.00 0.00 0.00 2.24
907 2838 8.796475 ACTACTAACCACTCTTCGTGTATAAAA 58.204 33.333 0.00 0.00 42.20 1.52
908 2839 7.880059 ACTAACCACTCTTCGTGTATAAAAC 57.120 36.000 0.00 0.00 42.20 2.43
909 2840 5.834239 AACCACTCTTCGTGTATAAAACG 57.166 39.130 3.41 3.41 42.20 3.60
915 2846 2.344504 TCGTGTATAAAACGACCGCA 57.655 45.000 7.61 0.00 44.58 5.69
916 2847 2.670479 TCGTGTATAAAACGACCGCAA 58.330 42.857 7.61 0.00 44.58 4.85
917 2848 3.252400 TCGTGTATAAAACGACCGCAAT 58.748 40.909 7.61 0.00 44.58 3.56
919 2850 5.992109 TCGTGTATAAAACGACCGCAATCG 61.992 45.833 7.61 5.12 44.58 3.34
922 2853 0.440758 TAAAACGACCGCAATCGCTG 59.559 50.000 6.52 0.00 46.22 5.18
939 2870 3.948719 GCAACCACTCCCCCGTCA 61.949 66.667 0.00 0.00 0.00 4.35
970 2902 4.437682 ACTCCAGATTCCAGAACAACAA 57.562 40.909 0.00 0.00 0.00 2.83
971 2903 4.137543 ACTCCAGATTCCAGAACAACAAC 58.862 43.478 0.00 0.00 0.00 3.32
972 2904 4.136796 CTCCAGATTCCAGAACAACAACA 58.863 43.478 0.00 0.00 0.00 3.33
973 2905 3.882888 TCCAGATTCCAGAACAACAACAC 59.117 43.478 0.00 0.00 0.00 3.32
974 2906 3.631686 CCAGATTCCAGAACAACAACACA 59.368 43.478 0.00 0.00 0.00 3.72
975 2907 4.498009 CCAGATTCCAGAACAACAACACAC 60.498 45.833 0.00 0.00 0.00 3.82
976 2908 4.096231 CAGATTCCAGAACAACAACACACA 59.904 41.667 0.00 0.00 0.00 3.72
977 2909 4.889409 AGATTCCAGAACAACAACACACAT 59.111 37.500 0.00 0.00 0.00 3.21
978 2910 6.017192 CAGATTCCAGAACAACAACACACATA 60.017 38.462 0.00 0.00 0.00 2.29
979 2911 5.749596 TTCCAGAACAACAACACACATAG 57.250 39.130 0.00 0.00 0.00 2.23
1033 2978 1.524482 CAGGCTAGGAAGGAGCACC 59.476 63.158 0.00 0.00 41.98 5.01
1260 3205 1.510383 CACACCTGAGGAGCTCGAG 59.490 63.158 4.99 8.45 32.35 4.04
1272 3217 1.832167 GCTCGAGCTGGAGGAGGAT 60.832 63.158 29.88 0.00 38.21 3.24
1281 3226 2.027377 GCTGGAGGAGGATGATATGGTG 60.027 54.545 0.00 0.00 0.00 4.17
1338 3283 0.034186 TTCCTGCATGGATGTGGGAC 60.034 55.000 5.83 0.00 45.68 4.46
1339 3284 1.206811 TCCTGCATGGATGTGGGACA 61.207 55.000 0.00 0.00 40.56 4.02
1340 3285 0.750546 CCTGCATGGATGTGGGACAG 60.751 60.000 0.00 0.00 37.09 3.51
1341 3286 0.034767 CTGCATGGATGTGGGACAGT 60.035 55.000 0.00 0.00 41.80 3.55
1342 3287 0.322726 TGCATGGATGTGGGACAGTG 60.323 55.000 0.00 0.00 41.80 3.66
1343 3288 1.033746 GCATGGATGTGGGACAGTGG 61.034 60.000 0.00 0.00 41.80 4.00
1344 3289 0.394762 CATGGATGTGGGACAGTGGG 60.395 60.000 0.00 0.00 41.80 4.61
1346 3291 1.200760 TGGATGTGGGACAGTGGGAG 61.201 60.000 0.00 0.00 41.80 4.30
1348 3293 1.568504 GATGTGGGACAGTGGGAGTA 58.431 55.000 0.00 0.00 41.80 2.59
1349 3294 1.482593 GATGTGGGACAGTGGGAGTAG 59.517 57.143 0.00 0.00 41.80 2.57
1350 3295 1.192146 TGTGGGACAGTGGGAGTAGC 61.192 60.000 0.00 0.00 41.80 3.58
1351 3296 0.905337 GTGGGACAGTGGGAGTAGCT 60.905 60.000 0.00 0.00 41.80 3.32
1352 3297 0.708209 TGGGACAGTGGGAGTAGCTA 59.292 55.000 0.00 0.00 0.00 3.32
1353 3298 1.342076 TGGGACAGTGGGAGTAGCTAG 60.342 57.143 0.00 0.00 0.00 3.42
1354 3299 1.404843 GGACAGTGGGAGTAGCTAGG 58.595 60.000 0.00 0.00 0.00 3.02
1355 3300 1.063867 GGACAGTGGGAGTAGCTAGGA 60.064 57.143 0.00 0.00 0.00 2.94
1356 3301 2.025898 GACAGTGGGAGTAGCTAGGAC 58.974 57.143 0.00 0.00 0.00 3.85
1357 3302 1.025812 CAGTGGGAGTAGCTAGGACG 58.974 60.000 0.00 0.00 0.00 4.79
1358 3303 0.917533 AGTGGGAGTAGCTAGGACGA 59.082 55.000 0.00 0.00 0.00 4.20
1359 3304 1.284198 AGTGGGAGTAGCTAGGACGAA 59.716 52.381 0.00 0.00 0.00 3.85
1360 3305 1.404748 GTGGGAGTAGCTAGGACGAAC 59.595 57.143 0.00 0.00 0.00 3.95
1361 3306 1.031235 GGGAGTAGCTAGGACGAACC 58.969 60.000 0.00 0.00 39.35 3.62
1389 3334 0.595095 GCTATGCTGTTATGCCCTGC 59.405 55.000 0.00 0.00 0.00 4.85
1438 3390 2.423185 CCGGTGCTAAATTTCTGATGCA 59.577 45.455 0.00 0.00 0.00 3.96
1450 3402 8.976986 AAATTTCTGATGCAAGAGTATGTTTC 57.023 30.769 0.00 0.00 0.00 2.78
1471 3423 8.102676 TGTTTCAACCATCTAGATTCATCTTCA 58.897 33.333 1.33 0.00 38.32 3.02
1487 3439 8.507470 TTCATCTTCATATCTATTTCGTCGTG 57.493 34.615 0.00 0.00 0.00 4.35
1514 3466 3.509575 TGAACCATGGTGCCTTTTATGTC 59.490 43.478 20.60 8.57 0.00 3.06
1529 3481 7.224753 GCCTTTTATGTCGAGTTCTATGAATCA 59.775 37.037 0.00 0.00 0.00 2.57
1561 3521 6.727824 ATTATATGACATACTGGCTTTCGC 57.272 37.500 0.00 0.00 0.00 4.70
1607 3567 7.733402 AAGGAGTATCTAGATAAGTGTCGAC 57.267 40.000 14.09 9.11 33.73 4.20
1643 3603 1.112113 TTCGATGCCAGAGTAGGGTC 58.888 55.000 0.00 0.00 0.00 4.46
1644 3604 1.101635 TCGATGCCAGAGTAGGGTCG 61.102 60.000 0.00 0.00 0.00 4.79
1645 3605 1.742768 GATGCCAGAGTAGGGTCGG 59.257 63.158 0.00 0.00 0.00 4.79
1646 3606 1.001760 ATGCCAGAGTAGGGTCGGT 59.998 57.895 0.00 0.00 0.00 4.69
1738 3699 6.928979 TGTTGAGAAATACAAAACCTTCGA 57.071 33.333 0.00 0.00 0.00 3.71
1739 3700 6.954944 TGTTGAGAAATACAAAACCTTCGAG 58.045 36.000 0.00 0.00 0.00 4.04
1740 3701 6.764085 TGTTGAGAAATACAAAACCTTCGAGA 59.236 34.615 0.00 0.00 0.00 4.04
1741 3702 7.444183 TGTTGAGAAATACAAAACCTTCGAGAT 59.556 33.333 0.00 0.00 0.00 2.75
1742 3703 7.979444 TGAGAAATACAAAACCTTCGAGATT 57.021 32.000 0.00 0.00 0.00 2.40
1743 3704 8.029642 TGAGAAATACAAAACCTTCGAGATTC 57.970 34.615 0.00 0.00 0.00 2.52
1744 3705 7.119262 TGAGAAATACAAAACCTTCGAGATTCC 59.881 37.037 0.00 0.00 0.00 3.01
1745 3706 6.940298 AGAAATACAAAACCTTCGAGATTCCA 59.060 34.615 0.00 0.00 0.00 3.53
1746 3707 7.447238 AGAAATACAAAACCTTCGAGATTCCAA 59.553 33.333 0.00 0.00 0.00 3.53
1747 3708 7.703058 AATACAAAACCTTCGAGATTCCAAT 57.297 32.000 0.00 0.00 0.00 3.16
1748 3709 8.801882 AATACAAAACCTTCGAGATTCCAATA 57.198 30.769 0.00 0.00 0.00 1.90
1749 3710 8.980481 ATACAAAACCTTCGAGATTCCAATAT 57.020 30.769 0.00 0.00 0.00 1.28
1750 3711 7.088589 ACAAAACCTTCGAGATTCCAATATG 57.911 36.000 0.00 0.00 0.00 1.78
1751 3712 6.095440 ACAAAACCTTCGAGATTCCAATATGG 59.905 38.462 0.00 0.00 39.43 2.74
1752 3713 5.630415 AACCTTCGAGATTCCAATATGGA 57.370 39.130 0.00 0.00 46.61 3.41
1767 3728 8.134202 TCCAATATGGACTACACCTACATATG 57.866 38.462 0.00 0.00 42.67 1.78
1768 3729 7.180229 TCCAATATGGACTACACCTACATATGG 59.820 40.741 7.80 0.00 42.67 2.74
1769 3730 7.038302 CCAATATGGACTACACCTACATATGGT 60.038 40.741 7.80 0.00 40.96 3.55
1778 3739 5.833406 CACCTACATATGGTGCAAAATGA 57.167 39.130 7.80 0.00 46.73 2.57
1779 3740 5.824429 CACCTACATATGGTGCAAAATGAG 58.176 41.667 7.80 0.00 46.73 2.90
1780 3741 5.589855 CACCTACATATGGTGCAAAATGAGA 59.410 40.000 7.80 0.00 46.73 3.27
1781 3742 5.824624 ACCTACATATGGTGCAAAATGAGAG 59.175 40.000 7.80 0.00 36.30 3.20
1782 3743 6.057533 CCTACATATGGTGCAAAATGAGAGA 58.942 40.000 7.80 0.00 0.00 3.10
1783 3744 6.543465 CCTACATATGGTGCAAAATGAGAGAA 59.457 38.462 7.80 0.00 0.00 2.87
1784 3745 7.230108 CCTACATATGGTGCAAAATGAGAGAAT 59.770 37.037 7.80 0.00 0.00 2.40
1785 3746 9.276590 CTACATATGGTGCAAAATGAGAGAATA 57.723 33.333 7.80 0.00 0.00 1.75
1786 3747 8.701908 ACATATGGTGCAAAATGAGAGAATAT 57.298 30.769 7.80 0.00 0.00 1.28
1787 3748 9.797642 ACATATGGTGCAAAATGAGAGAATATA 57.202 29.630 7.80 0.00 0.00 0.86
1844 3805 9.358406 TCGTATGTAGTTTATAGGGAAATCTCA 57.642 33.333 0.00 0.00 0.00 3.27
1845 3806 9.976511 CGTATGTAGTTTATAGGGAAATCTCAA 57.023 33.333 0.00 0.00 0.00 3.02
1914 3875 9.478019 CAAGTACTATATCACTTTTTCGCTTTG 57.522 33.333 0.00 0.00 32.72 2.77
1915 3876 8.773404 AGTACTATATCACTTTTTCGCTTTGT 57.227 30.769 0.00 0.00 0.00 2.83
1933 3894 6.477742 GCTTTGTGTTTGTTTCCTTTCATTC 58.522 36.000 0.00 0.00 0.00 2.67
2046 4007 9.423061 GGTATTATTTTCTTTTGCAAGTCATGT 57.577 29.630 0.00 0.00 0.00 3.21
2100 4062 9.118236 GTTACTATTCTTTTTGCAAGACATGTC 57.882 33.333 18.47 18.47 0.00 3.06
2136 4099 5.105554 ACACAATACAAAAACAGGCACTCAA 60.106 36.000 0.00 0.00 34.60 3.02
2153 4116 5.220854 GCACTCAAATACACACAGACACTTT 60.221 40.000 0.00 0.00 0.00 2.66
2160 4123 4.465632 ACACACAGACACTTTGTAGTCA 57.534 40.909 0.00 0.00 37.23 3.41
2169 4132 6.479990 CAGACACTTTGTAGTCAATGAGAACA 59.520 38.462 0.00 0.00 37.23 3.18
2185 4148 5.947503 GAGAACATCGTCTCATTCTGAAG 57.052 43.478 0.00 0.00 43.10 3.02
2186 4149 5.398603 AGAACATCGTCTCATTCTGAAGT 57.601 39.130 0.00 0.00 30.26 3.01
2187 4150 5.406649 AGAACATCGTCTCATTCTGAAGTC 58.593 41.667 0.00 0.00 30.26 3.01
2192 4155 7.495901 ACATCGTCTCATTCTGAAGTCATATT 58.504 34.615 0.00 0.00 0.00 1.28
2196 4159 6.075152 CGTCTCATTCTGAAGTCATATTGTCG 60.075 42.308 0.00 0.00 0.00 4.35
2197 4160 6.975197 GTCTCATTCTGAAGTCATATTGTCGA 59.025 38.462 0.00 0.00 0.00 4.20
2201 4164 9.816354 TCATTCTGAAGTCATATTGTCGAAATA 57.184 29.630 0.00 0.00 0.00 1.40
2235 4198 3.127589 TCGAGAAAATGCGAACACTCAA 58.872 40.909 0.00 0.00 33.04 3.02
2279 4245 1.004277 GGATAGGCCTGTTTCACCACA 59.996 52.381 17.99 0.00 0.00 4.17
2292 4258 2.692024 TCACCACAGGTAACCTAACCA 58.308 47.619 0.00 0.00 42.40 3.67
2296 4262 2.419574 CCACAGGTAACCTAACCATCCG 60.420 54.545 0.00 0.00 42.40 4.18
2310 4310 8.434392 ACCTAACCATCCGAGCTAATATTTTAA 58.566 33.333 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 7.355101 AGAAGACCACCTATTCTATACTCACA 58.645 38.462 0.00 0.00 31.63 3.58
53 54 8.618240 TCCAAAAGAAGACCACCTATTCTATA 57.382 34.615 0.00 0.00 33.05 1.31
121 122 1.186267 ACCACCTCTCTCCGTTGTCC 61.186 60.000 0.00 0.00 0.00 4.02
122 123 0.038159 CACCACCTCTCTCCGTTGTC 60.038 60.000 0.00 0.00 0.00 3.18
123 124 1.472662 CCACCACCTCTCTCCGTTGT 61.473 60.000 0.00 0.00 0.00 3.32
124 125 1.185618 TCCACCACCTCTCTCCGTTG 61.186 60.000 0.00 0.00 0.00 4.10
125 126 0.252284 ATCCACCACCTCTCTCCGTT 60.252 55.000 0.00 0.00 0.00 4.44
126 127 0.629596 TATCCACCACCTCTCTCCGT 59.370 55.000 0.00 0.00 0.00 4.69
127 128 1.615883 CATATCCACCACCTCTCTCCG 59.384 57.143 0.00 0.00 0.00 4.63
152 153 4.680237 CTCTGCGACGCCAACCCA 62.680 66.667 18.69 0.00 0.00 4.51
166 167 1.933765 ACATCCACCTCCTACCTCTCT 59.066 52.381 0.00 0.00 0.00 3.10
189 190 1.229145 CAGCATCCCCCAACCCAAA 60.229 57.895 0.00 0.00 0.00 3.28
191 192 3.671410 CCAGCATCCCCCAACCCA 61.671 66.667 0.00 0.00 0.00 4.51
199 200 0.324275 TTTAACCCAGCCAGCATCCC 60.324 55.000 0.00 0.00 0.00 3.85
274 275 2.123854 CGTCTCCTCCGATGGGGA 60.124 66.667 0.00 0.00 44.68 4.81
333 334 1.338769 GCAACCTAGACGGACAATGGT 60.339 52.381 0.00 0.00 36.31 3.55
335 336 2.386661 AGCAACCTAGACGGACAATG 57.613 50.000 0.00 0.00 36.31 2.82
338 339 2.367567 AGAAAAGCAACCTAGACGGACA 59.632 45.455 0.00 0.00 36.31 4.02
392 393 0.179189 CTCAAATCCGCCTCAAACGC 60.179 55.000 0.00 0.00 0.00 4.84
504 572 8.108172 CGTATGTATAAACATGATCAATACGCC 58.892 37.037 14.34 4.10 45.99 5.68
529 834 0.795735 AACGATTACTGGACGCGTCG 60.796 55.000 30.99 21.22 33.66 5.12
555 904 0.814010 ACAGCCACGGACAACAAGTC 60.814 55.000 0.00 0.00 46.83 3.01
623 2313 2.053244 AGAGCCTGCCACTGCTTATAT 58.947 47.619 0.00 0.00 38.11 0.86
645 2575 0.678048 ATTCAAAGCGAGCACCTCCC 60.678 55.000 0.00 0.00 0.00 4.30
721 2651 1.151777 GCGTATTGCAGCGAGCCTTA 61.152 55.000 10.76 0.00 45.45 2.69
736 2666 1.080839 GGTACGGAAACACGGCGTA 60.081 57.895 14.22 0.00 38.39 4.42
782 2712 3.065925 GGCTGCATGAGTCAAAGATTACC 59.934 47.826 0.50 0.00 0.00 2.85
797 2727 0.990374 AAGACTGAAGAGGGCTGCAT 59.010 50.000 0.50 0.00 0.00 3.96
875 2806 7.310664 CACGAAGAGTGGTTAGTAGTAATTCA 58.689 38.462 0.00 0.00 46.77 2.57
915 2846 1.675641 GGGAGTGGTTGCAGCGATT 60.676 57.895 0.00 0.00 0.00 3.34
916 2847 2.045926 GGGAGTGGTTGCAGCGAT 60.046 61.111 0.00 0.00 0.00 4.58
917 2848 4.329545 GGGGAGTGGTTGCAGCGA 62.330 66.667 0.00 0.00 0.00 4.93
922 2853 3.948719 TGACGGGGGAGTGGTTGC 61.949 66.667 0.00 0.00 0.00 4.17
924 2855 0.472352 TTAGTGACGGGGGAGTGGTT 60.472 55.000 0.00 0.00 0.00 3.67
926 2857 1.189524 TGTTAGTGACGGGGGAGTGG 61.190 60.000 0.00 0.00 0.00 4.00
931 2862 1.346722 AGTTCTTGTTAGTGACGGGGG 59.653 52.381 0.00 0.00 0.00 5.40
939 2870 5.544176 TCTGGAATCTGGAGTTCTTGTTAGT 59.456 40.000 0.00 0.00 0.00 2.24
970 2902 3.408634 GTTTAGTGGTGGCTATGTGTGT 58.591 45.455 0.00 0.00 0.00 3.72
971 2903 2.747446 GGTTTAGTGGTGGCTATGTGTG 59.253 50.000 0.00 0.00 0.00 3.82
972 2904 2.290705 GGGTTTAGTGGTGGCTATGTGT 60.291 50.000 0.00 0.00 0.00 3.72
973 2905 2.365582 GGGTTTAGTGGTGGCTATGTG 58.634 52.381 0.00 0.00 0.00 3.21
974 2906 1.065709 CGGGTTTAGTGGTGGCTATGT 60.066 52.381 0.00 0.00 0.00 2.29
975 2907 1.208535 TCGGGTTTAGTGGTGGCTATG 59.791 52.381 0.00 0.00 0.00 2.23
976 2908 1.575419 TCGGGTTTAGTGGTGGCTAT 58.425 50.000 0.00 0.00 0.00 2.97
977 2909 1.350071 TTCGGGTTTAGTGGTGGCTA 58.650 50.000 0.00 0.00 0.00 3.93
978 2910 0.475044 TTTCGGGTTTAGTGGTGGCT 59.525 50.000 0.00 0.00 0.00 4.75
979 2911 0.594602 GTTTCGGGTTTAGTGGTGGC 59.405 55.000 0.00 0.00 0.00 5.01
1234 3179 1.979155 CCTCAGGTGTGCTCTCCGA 60.979 63.158 1.49 2.35 33.02 4.55
1236 3181 1.896694 CTCCTCAGGTGTGCTCTCC 59.103 63.158 0.00 0.00 0.00 3.71
1260 3205 2.027377 CACCATATCATCCTCCTCCAGC 60.027 54.545 0.00 0.00 0.00 4.85
1272 3217 5.508567 TGCTCAAAGAAATCCACCATATCA 58.491 37.500 0.00 0.00 0.00 2.15
1281 3226 4.441079 CCATCCACATGCTCAAAGAAATCC 60.441 45.833 0.00 0.00 0.00 3.01
1321 3266 0.750546 CTGTCCCACATCCATGCAGG 60.751 60.000 0.00 0.00 39.47 4.85
1338 3283 1.025812 CGTCCTAGCTACTCCCACTG 58.974 60.000 0.00 0.00 0.00 3.66
1339 3284 0.917533 TCGTCCTAGCTACTCCCACT 59.082 55.000 0.00 0.00 0.00 4.00
1340 3285 1.404748 GTTCGTCCTAGCTACTCCCAC 59.595 57.143 0.00 0.00 0.00 4.61
1341 3286 1.684248 GGTTCGTCCTAGCTACTCCCA 60.684 57.143 0.00 0.00 0.00 4.37
1342 3287 1.031235 GGTTCGTCCTAGCTACTCCC 58.969 60.000 0.00 0.00 0.00 4.30
1343 3288 2.055684 AGGTTCGTCCTAGCTACTCC 57.944 55.000 0.00 0.00 46.10 3.85
1357 3302 1.491505 GCATAGCGGCGAAGAGGTTC 61.492 60.000 12.98 0.00 0.00 3.62
1358 3303 1.521681 GCATAGCGGCGAAGAGGTT 60.522 57.895 12.98 0.00 0.00 3.50
1359 3304 2.107141 GCATAGCGGCGAAGAGGT 59.893 61.111 12.98 0.00 0.00 3.85
1360 3305 1.953138 CAGCATAGCGGCGAAGAGG 60.953 63.158 12.98 0.00 39.27 3.69
1361 3306 0.807667 AACAGCATAGCGGCGAAGAG 60.808 55.000 12.98 0.00 39.27 2.85
1362 3307 0.458260 TAACAGCATAGCGGCGAAGA 59.542 50.000 12.98 0.00 39.27 2.87
1363 3308 1.193203 CATAACAGCATAGCGGCGAAG 59.807 52.381 12.98 0.00 39.27 3.79
1371 3316 0.870393 CGCAGGGCATAACAGCATAG 59.130 55.000 0.00 0.00 35.83 2.23
1372 3317 1.165907 GCGCAGGGCATAACAGCATA 61.166 55.000 0.30 0.00 42.87 3.14
1389 3334 3.063588 TCGATACTTATCTAGATGCCGCG 59.936 47.826 15.79 0.00 0.00 6.46
1438 3390 9.606631 GAATCTAGATGGTTGAAACATACTCTT 57.393 33.333 5.86 0.00 0.00 2.85
1471 3423 7.201496 GGTTCAAACACACGACGAAATAGATAT 60.201 37.037 0.00 0.00 0.00 1.63
1487 3439 1.039856 AGGCACCATGGTTCAAACAC 58.960 50.000 16.84 0.00 0.00 3.32
1607 3567 6.034898 GGCATCGAAAATTTGACACCTTAATG 59.965 38.462 0.00 0.00 0.00 1.90
1714 3675 7.444183 TCTCGAAGGTTTTGTATTTCTCAACAT 59.556 33.333 0.00 0.00 0.00 2.71
1717 3678 7.979444 ATCTCGAAGGTTTTGTATTTCTCAA 57.021 32.000 0.00 0.00 0.00 3.02
1718 3679 7.119262 GGAATCTCGAAGGTTTTGTATTTCTCA 59.881 37.037 0.00 0.00 0.00 3.27
1720 3681 6.940298 TGGAATCTCGAAGGTTTTGTATTTCT 59.060 34.615 0.00 0.00 0.00 2.52
1721 3682 7.141100 TGGAATCTCGAAGGTTTTGTATTTC 57.859 36.000 0.00 0.00 0.00 2.17
1722 3683 7.519032 TTGGAATCTCGAAGGTTTTGTATTT 57.481 32.000 0.00 0.00 0.00 1.40
1723 3684 7.703058 ATTGGAATCTCGAAGGTTTTGTATT 57.297 32.000 0.00 0.00 0.00 1.89
1724 3685 8.840321 CATATTGGAATCTCGAAGGTTTTGTAT 58.160 33.333 0.00 0.00 0.00 2.29
1725 3686 7.282224 CCATATTGGAATCTCGAAGGTTTTGTA 59.718 37.037 0.00 0.00 40.96 2.41
1726 3687 6.095440 CCATATTGGAATCTCGAAGGTTTTGT 59.905 38.462 0.00 0.00 40.96 2.83
1727 3688 6.318648 TCCATATTGGAATCTCGAAGGTTTTG 59.681 38.462 0.00 0.00 45.00 2.44
1728 3689 6.423182 TCCATATTGGAATCTCGAAGGTTTT 58.577 36.000 0.00 0.00 45.00 2.43
1729 3690 6.001449 TCCATATTGGAATCTCGAAGGTTT 57.999 37.500 0.00 0.00 45.00 3.27
1730 3691 5.630415 TCCATATTGGAATCTCGAAGGTT 57.370 39.130 0.00 0.00 45.00 3.50
1742 3703 7.180229 CCATATGTAGGTGTAGTCCATATTGGA 59.820 40.741 1.24 0.00 45.98 3.53
1743 3704 7.038302 ACCATATGTAGGTGTAGTCCATATTGG 60.038 40.741 1.24 0.00 38.13 3.16
1744 3705 7.907389 ACCATATGTAGGTGTAGTCCATATTG 58.093 38.462 1.24 0.00 38.13 1.90
1757 3718 5.754782 TCTCATTTTGCACCATATGTAGGT 58.245 37.500 1.24 0.00 40.85 3.08
1758 3719 6.057533 TCTCTCATTTTGCACCATATGTAGG 58.942 40.000 1.24 0.00 0.00 3.18
1759 3720 7.558161 TTCTCTCATTTTGCACCATATGTAG 57.442 36.000 1.24 0.00 0.00 2.74
1760 3721 9.797642 ATATTCTCTCATTTTGCACCATATGTA 57.202 29.630 1.24 0.00 0.00 2.29
1761 3722 8.701908 ATATTCTCTCATTTTGCACCATATGT 57.298 30.769 1.24 0.00 0.00 2.29
1818 3779 9.358406 TGAGATTTCCCTATAAACTACATACGA 57.642 33.333 0.00 0.00 0.00 3.43
1819 3780 9.976511 TTGAGATTTCCCTATAAACTACATACG 57.023 33.333 0.00 0.00 0.00 3.06
1858 3819 8.656806 TGATTCATACTCCCTCCGTTATTAAAT 58.343 33.333 0.00 0.00 0.00 1.40
1859 3820 8.025270 TGATTCATACTCCCTCCGTTATTAAA 57.975 34.615 0.00 0.00 0.00 1.52
1860 3821 7.606135 TGATTCATACTCCCTCCGTTATTAA 57.394 36.000 0.00 0.00 0.00 1.40
1861 3822 7.606135 TTGATTCATACTCCCTCCGTTATTA 57.394 36.000 0.00 0.00 0.00 0.98
1862 3823 6.494666 TTGATTCATACTCCCTCCGTTATT 57.505 37.500 0.00 0.00 0.00 1.40
1863 3824 6.494666 TTTGATTCATACTCCCTCCGTTAT 57.505 37.500 0.00 0.00 0.00 1.89
1864 3825 5.943349 TTTGATTCATACTCCCTCCGTTA 57.057 39.130 0.00 0.00 0.00 3.18
1865 3826 4.837093 TTTGATTCATACTCCCTCCGTT 57.163 40.909 0.00 0.00 0.00 4.44
1866 3827 4.019681 TGTTTTGATTCATACTCCCTCCGT 60.020 41.667 0.00 0.00 0.00 4.69
1867 3828 4.513442 TGTTTTGATTCATACTCCCTCCG 58.487 43.478 0.00 0.00 0.00 4.63
1868 3829 5.946377 ACTTGTTTTGATTCATACTCCCTCC 59.054 40.000 0.00 0.00 0.00 4.30
1869 3830 7.824779 AGTACTTGTTTTGATTCATACTCCCTC 59.175 37.037 0.00 0.00 0.00 4.30
1870 3831 7.690256 AGTACTTGTTTTGATTCATACTCCCT 58.310 34.615 0.00 0.00 0.00 4.20
1871 3832 7.923414 AGTACTTGTTTTGATTCATACTCCC 57.077 36.000 0.00 0.00 0.00 4.30
1903 3864 4.991687 AGGAAACAAACACAAAGCGAAAAA 59.008 33.333 0.00 0.00 0.00 1.94
1914 3875 8.879260 CTTTTTGAATGAAAGGAAACAAACAC 57.121 30.769 0.00 0.00 31.94 3.32
1995 3956 7.924412 CCATAGCAGCAATCAGAACAAAATAAT 59.076 33.333 0.00 0.00 0.00 1.28
2006 3967 8.790718 AGAAAATAATACCATAGCAGCAATCAG 58.209 33.333 0.00 0.00 0.00 2.90
2008 3969 9.971922 AAAGAAAATAATACCATAGCAGCAATC 57.028 29.630 0.00 0.00 0.00 2.67
2068 4029 9.344772 TCTTGCAAAAAGAATAGTAACAGGTTA 57.655 29.630 0.00 0.00 0.00 2.85
2075 4037 9.066892 AGACATGTCTTGCAAAAAGAATAGTAA 57.933 29.630 22.89 0.00 36.31 2.24
2109 4071 6.169800 AGTGCCTGTTTTTGTATTGTGTTTT 58.830 32.000 0.00 0.00 0.00 2.43
2122 4085 4.400884 TGTGTGTATTTGAGTGCCTGTTTT 59.599 37.500 0.00 0.00 0.00 2.43
2125 4088 3.141398 CTGTGTGTATTTGAGTGCCTGT 58.859 45.455 0.00 0.00 0.00 4.00
2128 4091 3.058914 GTGTCTGTGTGTATTTGAGTGCC 60.059 47.826 0.00 0.00 0.00 5.01
2129 4092 3.809832 AGTGTCTGTGTGTATTTGAGTGC 59.190 43.478 0.00 0.00 0.00 4.40
2136 4099 6.578944 TGACTACAAAGTGTCTGTGTGTATT 58.421 36.000 3.18 0.00 32.42 1.89
2153 4116 5.183140 TGAGACGATGTTCTCATTGACTACA 59.817 40.000 0.00 0.15 45.79 2.74
2179 4142 7.782049 AGGTATTTCGACAATATGACTTCAGA 58.218 34.615 0.00 0.00 0.00 3.27
2192 4155 9.459640 CTCGAATTTATTCTAGGTATTTCGACA 57.540 33.333 13.70 0.00 34.69 4.35
2201 4164 7.494625 TCGCATTTTCTCGAATTTATTCTAGGT 59.505 33.333 4.71 0.00 34.69 3.08
2235 4198 6.176183 CCAGGTTCAAGTCATTCACTTATCT 58.824 40.000 0.00 0.00 44.14 1.98
2267 4233 3.208747 AGGTTACCTGTGGTGAAACAG 57.791 47.619 1.74 0.00 45.93 3.16
2279 4245 1.761198 GCTCGGATGGTTAGGTTACCT 59.239 52.381 9.57 9.57 39.04 3.08
2319 4319 7.778853 AGTCATGCAAATCAAAGAGATCCTTAT 59.221 33.333 0.00 0.00 35.39 1.73


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

AutoCloner maintained by Alex Coulton.