Multiple sequence alignment - TraesCS2D01G352800

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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 TraesCS2D01G352800 chr2D 100.000 6859 0 0 1 6859 451006112 450999254 0.000000e+00 12667
1 TraesCS2D01G352800 chr2A 94.676 5071 179 52 1414 6401 598610366 598615428 0.000000e+00 7784
2 TraesCS2D01G352800 chr2A 84.417 815 53 30 610 1414 598609583 598610333 0.000000e+00 734
3 TraesCS2D01G352800 chr2A 90.239 461 31 6 6399 6859 598615466 598615912 2.130000e-164 590
4 TraesCS2D01G352800 chr2B 91.136 3802 225 70 1 3746 531143868 531140123 0.000000e+00 5051
5 TraesCS2D01G352800 chr2B 96.771 1084 33 2 3745 4826 531139825 531138742 0.000000e+00 1807
6 TraesCS2D01G352800 chr2B 93.942 1106 40 12 4853 5933 531138369 531137266 0.000000e+00 1646
7 TraesCS2D01G352800 chr2B 92.639 883 40 12 5986 6859 531137266 531136400 0.000000e+00 1247
8 TraesCS2D01G352800 chr2B 83.226 155 11 7 5235 5387 531138088 531138229 2.010000e-25 128
9 TraesCS2D01G352800 chr3D 90.055 181 12 2 6606 6781 517004129 517004308 5.350000e-56 230
10 TraesCS2D01G352800 chr3D 91.667 108 6 2 6518 6625 517004011 517004115 5.540000e-31 147
11 TraesCS2D01G352800 chr3B 91.057 123 7 2 6741 6859 680237642 680237520 5.500000e-36 163
12 TraesCS2D01G352800 chr3B 93.506 77 5 0 6521 6597 680245896 680245820 1.560000e-21 115


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 TraesCS2D01G352800 chr2D 450999254 451006112 6858 True 12667.00 12667 100.000000 1 6859 1 chr2D.!!$R1 6858
1 TraesCS2D01G352800 chr2A 598609583 598615912 6329 False 3036.00 7784 89.777333 610 6859 3 chr2A.!!$F1 6249
2 TraesCS2D01G352800 chr2B 531136400 531143868 7468 True 2437.75 5051 93.622000 1 6859 4 chr2B.!!$R1 6858

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
86 87 0.248012 TGTAGGCACACATACACCCG 59.752 55.000 0.0 0.0 0.0 5.28 F
986 1019 0.340208 TCTCTTTCCCTCTCTCCCCC 59.660 60.000 0.0 0.0 0.0 5.40 F
2012 2102 0.036164 TGTTGCTGGCGGTATGAAGT 59.964 50.000 0.0 0.0 0.0 3.01 F
2580 2677 2.807967 GCTGTAGAAACACTGTCATGCA 59.192 45.455 0.0 0.0 0.0 3.96 F
3692 3798 3.360867 TGTTCTTTGACATGGTGGTTGT 58.639 40.909 0.0 0.0 0.0 3.32 F
5347 6123 0.034896 CACCCGCACTAAACTGGACT 59.965 55.000 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1238 1271 0.869730 GAAAACCGAAGCCTAACGCA 59.130 50.000 0.00 0.0 41.38 5.24 R
2024 2114 1.899814 TGGCTGACGATGGTAGTTTCT 59.100 47.619 0.00 0.0 0.00 2.52 R
3279 3378 0.320683 TCGCACCAGACCATGAAGTG 60.321 55.000 0.00 0.0 0.00 3.16 R
4404 4813 1.553248 CGTAGAAACATCCCCACCTCA 59.447 52.381 0.00 0.0 0.00 3.86 R
5585 6361 0.175989 GGACAGCTTAGGACCTTCCG 59.824 60.000 0.00 0.0 42.75 4.30 R
6517 7379 0.396435 CACTTGCCGGCCTCCATATA 59.604 55.000 26.77 0.0 0.00 0.86 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
20 21 2.432628 GGGAGCGGTTGTGTCTCG 60.433 66.667 0.00 0.00 0.00 4.04
52 53 3.438781 ACACACAAGCACGTATTAATGGG 59.561 43.478 0.00 0.00 0.00 4.00
85 86 2.093181 TCATGTAGGCACACATACACCC 60.093 50.000 4.66 0.00 37.02 4.61
86 87 0.248012 TGTAGGCACACATACACCCG 59.752 55.000 0.00 0.00 0.00 5.28
96 97 3.181485 ACACATACACCCGTTTTTGTTGG 60.181 43.478 0.00 0.00 0.00 3.77
97 98 3.025262 ACATACACCCGTTTTTGTTGGT 58.975 40.909 0.00 0.00 0.00 3.67
98 99 3.447944 ACATACACCCGTTTTTGTTGGTT 59.552 39.130 0.00 0.00 0.00 3.67
99 100 4.081586 ACATACACCCGTTTTTGTTGGTTT 60.082 37.500 0.00 0.00 0.00 3.27
100 101 3.404224 ACACCCGTTTTTGTTGGTTTT 57.596 38.095 0.00 0.00 0.00 2.43
101 102 4.532314 ACACCCGTTTTTGTTGGTTTTA 57.468 36.364 0.00 0.00 0.00 1.52
185 186 7.692908 ATTTTGTAGAAAACACCGTGAATTG 57.307 32.000 5.28 0.00 38.00 2.32
191 192 5.912892 AGAAAACACCGTGAATTGGAAAAT 58.087 33.333 5.28 0.00 0.00 1.82
200 201 5.220453 CCGTGAATTGGAAAATTGCTAATGC 60.220 40.000 0.00 0.00 40.20 3.56
267 268 9.739276 ATACCAGTCAAAATAATTTCTCTGACA 57.261 29.630 10.95 0.00 32.56 3.58
268 269 8.641498 ACCAGTCAAAATAATTTCTCTGACAT 57.359 30.769 10.95 0.00 32.56 3.06
269 270 9.082313 ACCAGTCAAAATAATTTCTCTGACATT 57.918 29.630 10.95 0.00 32.56 2.71
297 298 6.695292 AAATGTTCATGCATCTCGAAAAAC 57.305 33.333 0.00 0.00 0.00 2.43
298 299 4.159377 TGTTCATGCATCTCGAAAAACC 57.841 40.909 0.00 0.00 0.00 3.27
300 301 4.218200 TGTTCATGCATCTCGAAAAACCAT 59.782 37.500 0.00 0.00 0.00 3.55
301 302 5.414144 TGTTCATGCATCTCGAAAAACCATA 59.586 36.000 0.00 0.00 0.00 2.74
302 303 5.484173 TCATGCATCTCGAAAAACCATAC 57.516 39.130 0.00 0.00 0.00 2.39
304 305 5.589855 TCATGCATCTCGAAAAACCATACAT 59.410 36.000 0.00 0.00 0.00 2.29
305 306 5.233957 TGCATCTCGAAAAACCATACATG 57.766 39.130 0.00 0.00 0.00 3.21
306 307 4.940654 TGCATCTCGAAAAACCATACATGA 59.059 37.500 0.00 0.00 0.00 3.07
307 308 5.589855 TGCATCTCGAAAAACCATACATGAT 59.410 36.000 0.00 0.00 0.00 2.45
308 309 6.095300 TGCATCTCGAAAAACCATACATGATT 59.905 34.615 0.00 0.00 0.00 2.57
309 310 6.974622 GCATCTCGAAAAACCATACATGATTT 59.025 34.615 0.00 0.00 0.00 2.17
483 504 4.320608 AATTCAGCGTGTGTTGGAAAAT 57.679 36.364 0.00 0.00 0.00 1.82
758 784 2.812011 CGGAAGAAAACCGGTGAAAGAT 59.188 45.455 8.52 0.00 45.65 2.40
822 851 9.976255 TGAGAACGAAAATAATAACAATAACCG 57.024 29.630 0.00 0.00 0.00 4.44
823 852 9.977762 GAGAACGAAAATAATAACAATAACCGT 57.022 29.630 0.00 0.00 0.00 4.83
844 873 5.679792 CCGTACAAAACCGAAAGAGAAAAAG 59.320 40.000 0.00 0.00 0.00 2.27
883 913 0.464452 GAGCTACAGTATTGGGCCGT 59.536 55.000 0.00 0.00 0.00 5.68
899 929 2.740714 CGTTCCACTAGCCTTGCGC 61.741 63.158 0.00 0.00 37.98 6.09
985 1018 1.788229 CTCTCTTTCCCTCTCTCCCC 58.212 60.000 0.00 0.00 0.00 4.81
986 1019 0.340208 TCTCTTTCCCTCTCTCCCCC 59.660 60.000 0.00 0.00 0.00 5.40
988 1021 0.496382 TCTTTCCCTCTCTCCCCCAA 59.504 55.000 0.00 0.00 0.00 4.12
989 1022 1.132201 TCTTTCCCTCTCTCCCCCAAA 60.132 52.381 0.00 0.00 0.00 3.28
990 1023 1.283321 CTTTCCCTCTCTCCCCCAAAG 59.717 57.143 0.00 0.00 0.00 2.77
991 1024 1.208165 TTCCCTCTCTCCCCCAAAGC 61.208 60.000 0.00 0.00 0.00 3.51
1095 1128 2.539688 CGCTTGCTTCATAGTCGCATTA 59.460 45.455 0.00 0.00 33.15 1.90
1198 1231 0.394899 CCTGATGCTTCCCCTTCACC 60.395 60.000 0.00 0.00 0.00 4.02
1210 1243 2.654863 CCCTTCACCTTTGTGTCTGTT 58.345 47.619 0.00 0.00 43.26 3.16
1218 1251 5.128171 TCACCTTTGTGTCTGTTAGTACTGT 59.872 40.000 5.39 0.00 43.26 3.55
1238 1271 2.351706 TTTTCCCCGCACTAGTTTGT 57.648 45.000 0.00 0.00 0.00 2.83
1339 1372 3.360533 CATCTCATTTCTTGTGATGCGC 58.639 45.455 0.00 0.00 44.70 6.09
1350 1383 0.455410 GTGATGCGCCATGCCTTTTA 59.545 50.000 4.18 0.00 45.60 1.52
1390 1423 8.743714 AGGATGAAAGTGTTCAATTATTCTTCC 58.256 33.333 9.12 9.12 46.66 3.46
1416 1482 3.764434 TGTTGAAACTAAAGGTTGGTGCA 59.236 39.130 0.00 0.00 38.29 4.57
1596 1667 9.659830 ATGACTTTGAATACGTTGTTAAGAAAC 57.340 29.630 0.00 0.00 36.07 2.78
1685 1757 8.518430 ACAACTTACCATACATATGCATTTGA 57.482 30.769 21.91 7.71 32.40 2.69
1701 1773 7.523293 TGCATTTGAAAATGAGAAGACCTAA 57.477 32.000 17.78 0.00 46.72 2.69
1739 1811 4.322198 CCAAAATTACTTCATGTGCTGGCT 60.322 41.667 0.00 0.00 0.00 4.75
1786 1858 9.770097 ACTAATATTGACTCAGTGTATTCATGG 57.230 33.333 0.00 0.00 0.00 3.66
1787 1859 9.770097 CTAATATTGACTCAGTGTATTCATGGT 57.230 33.333 0.00 0.00 0.00 3.55
1802 1888 4.974645 TCATGGTACTGAACTGGAGTTT 57.025 40.909 0.00 0.00 38.56 2.66
1839 1925 1.376424 CGAATGAGCAGCTGTGGGT 60.376 57.895 16.64 0.00 0.00 4.51
1896 1982 6.102615 ACACCAACCCACAGATATATTGGTAT 59.897 38.462 6.16 0.00 46.18 2.73
1900 1987 8.923270 CCAACCCACAGATATATTGGTATTTTT 58.077 33.333 2.06 0.00 33.41 1.94
1959 2049 9.085645 TGATTCCTACTCTGTTTACTAAGTTGA 57.914 33.333 0.00 0.00 0.00 3.18
2002 2092 1.407258 TGGTAAGTGTTTGTTGCTGGC 59.593 47.619 0.00 0.00 0.00 4.85
2004 2094 0.665835 TAAGTGTTTGTTGCTGGCGG 59.334 50.000 0.00 0.00 0.00 6.13
2012 2102 0.036164 TGTTGCTGGCGGTATGAAGT 59.964 50.000 0.00 0.00 0.00 3.01
2024 2114 4.396790 GCGGTATGAAGTTGGAATTTGGTA 59.603 41.667 0.00 0.00 0.00 3.25
2032 2122 8.161699 TGAAGTTGGAATTTGGTAGAAACTAC 57.838 34.615 0.00 0.00 0.00 2.73
2033 2123 7.229907 TGAAGTTGGAATTTGGTAGAAACTACC 59.770 37.037 17.80 17.80 38.07 3.18
2041 2131 4.713824 TGGTAGAAACTACCATCGTCAG 57.286 45.455 21.84 0.00 42.21 3.51
2149 2239 6.749923 ATAAAAGGATGTCTTCTCAACAGC 57.250 37.500 0.00 0.00 33.94 4.40
2166 2256 3.542712 CAGCGCTACTGTTTTGTGAAT 57.457 42.857 10.99 0.00 41.86 2.57
2272 2362 7.534723 TCTGCACTAGGAGTAAACTTTAGAA 57.465 36.000 0.00 0.00 34.40 2.10
2580 2677 2.807967 GCTGTAGAAACACTGTCATGCA 59.192 45.455 0.00 0.00 0.00 3.96
2646 2743 9.974980 CAATATTGTTTTGTTTAGTAACACCCT 57.025 29.630 7.32 0.00 43.66 4.34
2647 2744 9.974980 AATATTGTTTTGTTTAGTAACACCCTG 57.025 29.630 0.00 0.00 43.66 4.45
3117 3216 9.301153 GTTGTATATTTGGTTGATTGTCCAATC 57.699 33.333 12.10 12.10 45.55 2.67
3345 3444 5.546499 ACTTTGGAAGGATCACAAGGTAGTA 59.454 40.000 0.00 0.00 33.47 1.82
3382 3481 5.900123 ACTCCATTAGCTACCTCAATGTACT 59.100 40.000 0.00 0.00 0.00 2.73
3400 3500 5.666462 TGTACTGACTTGTAGCTGTTTTCA 58.334 37.500 0.00 0.00 0.00 2.69
3402 3502 7.438564 TGTACTGACTTGTAGCTGTTTTCATA 58.561 34.615 0.00 0.00 0.00 2.15
3403 3503 7.929245 TGTACTGACTTGTAGCTGTTTTCATAA 59.071 33.333 0.00 0.00 0.00 1.90
3565 3671 5.721232 AGTGCTACCACATTACTCTGTTAC 58.279 41.667 0.00 0.00 44.53 2.50
3692 3798 3.360867 TGTTCTTTGACATGGTGGTTGT 58.639 40.909 0.00 0.00 0.00 3.32
3736 3843 9.410556 GACACAAATTATTTGAGCAACACTTAT 57.589 29.630 22.53 0.00 43.26 1.73
3865 4274 9.114965 CGAATTATATTCTACAGGTAGTTCACG 57.885 37.037 6.37 0.00 34.84 4.35
4305 4714 9.899661 TTCTACATGCAAGTTATATTAACTGGT 57.100 29.630 0.00 0.00 0.00 4.00
4404 4813 4.949856 GGTAATTGTCCATTGACTCCACAT 59.050 41.667 0.00 0.00 42.28 3.21
4598 5007 7.928706 CCACCATCCTTCACTATTCTACTAAAG 59.071 40.741 0.00 0.00 0.00 1.85
4689 5098 4.271696 AGTTGCAGCACTTGACTACATA 57.728 40.909 2.55 0.00 0.00 2.29
4970 5725 1.676635 GAGCACCTGATTGGCTGCA 60.677 57.895 0.50 0.00 41.81 4.41
4989 5744 3.033185 GCACACGTGTGTTTTATGTGTC 58.967 45.455 40.10 21.38 44.15 3.67
5056 5811 2.541233 AGTGCAGGAGTATCTCAGGT 57.459 50.000 0.00 0.00 33.73 4.00
5117 5875 7.856145 AAAGTCAGTTTGGAATAGCTCTATG 57.144 36.000 0.00 0.00 0.00 2.23
5347 6123 0.034896 CACCCGCACTAAACTGGACT 59.965 55.000 0.00 0.00 0.00 3.85
5418 6194 1.739466 CCTGCGCATGTGAAGTTATGT 59.261 47.619 12.24 0.00 0.00 2.29
5533 6309 6.759497 ACTAAGTCCTGTTGCATTTAATCC 57.241 37.500 0.00 0.00 0.00 3.01
5585 6361 7.012989 TGGCTTACTTGAAAAAGGAGAACTTAC 59.987 37.037 0.00 0.00 38.85 2.34
5679 6460 6.146347 TGAAAATGTCAAATCACATGCACATG 59.854 34.615 9.06 9.06 37.07 3.21
5789 6570 3.596066 GAGCAAGGGCAGAGCACGA 62.596 63.158 0.00 0.00 44.61 4.35
6044 6825 8.519526 TGAAAAATATGTGTTGTATGAAGACCC 58.480 33.333 0.00 0.00 0.00 4.46
6123 6909 6.127111 CCCTTCCTACCCTAGAGTTAACTTTC 60.127 46.154 10.02 0.00 0.00 2.62
6303 7113 5.541953 TGCTGCTCATATCATTCTGTAGT 57.458 39.130 0.00 0.00 0.00 2.73
6427 7289 4.457257 GCTCTAGTGATGCCTTGAAAGTTT 59.543 41.667 0.00 0.00 0.00 2.66
6537 7399 2.965716 ATATGGAGGCCGGCAAGTGC 62.966 60.000 30.85 17.77 41.14 4.40
6670 7532 2.290641 CCTGGAAGTTGTTATATGCGCC 59.709 50.000 4.18 0.00 0.00 6.53
6750 7612 9.282247 CATACAATGTTCAATTTCTTCAGCTAC 57.718 33.333 0.00 0.00 0.00 3.58
6752 7614 7.715657 ACAATGTTCAATTTCTTCAGCTACAA 58.284 30.769 0.00 0.00 0.00 2.41
6818 7680 3.181461 ACGGCATCCCTCATTTTCTCTAG 60.181 47.826 0.00 0.00 0.00 2.43
6823 7685 6.429385 GGCATCCCTCATTTTCTCTAGTAATG 59.571 42.308 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.305922 GCTTGTGTGTCACTGCAGAC 59.694 55.000 23.35 10.19 35.77 3.51
52 53 2.746362 GCCTACATGATTATGGCTCAGC 59.254 50.000 0.00 0.00 40.36 4.26
54 55 3.136260 TGTGCCTACATGATTATGGCTCA 59.864 43.478 0.00 9.33 43.57 4.26
57 58 3.213506 TGTGTGCCTACATGATTATGGC 58.786 45.455 0.00 6.01 43.49 4.40
67 68 0.248012 CGGGTGTATGTGTGCCTACA 59.752 55.000 0.00 0.00 34.63 2.74
157 158 8.789881 TTCACGGTGTTTTCTACAAAATTATG 57.210 30.769 8.17 0.00 38.80 1.90
158 159 9.974980 AATTCACGGTGTTTTCTACAAAATTAT 57.025 25.926 8.17 0.00 38.80 1.28
159 160 9.239002 CAATTCACGGTGTTTTCTACAAAATTA 57.761 29.630 8.17 0.00 38.80 1.40
168 169 4.993029 TTTCCAATTCACGGTGTTTTCT 57.007 36.364 8.17 0.00 0.00 2.52
169 170 6.418141 CAATTTTCCAATTCACGGTGTTTTC 58.582 36.000 8.17 0.00 29.41 2.29
272 273 7.307337 GGTTTTTCGAGATGCATGAACATTTTT 60.307 33.333 2.46 0.00 0.00 1.94
273 274 6.146021 GGTTTTTCGAGATGCATGAACATTTT 59.854 34.615 2.46 0.00 0.00 1.82
341 342 8.989653 ACATTTCTTTTGAACGGTAAGAAAAA 57.010 26.923 16.25 5.71 45.56 1.94
345 346 8.441312 ACTTACATTTCTTTTGAACGGTAAGA 57.559 30.769 21.86 0.00 45.80 2.10
346 347 9.511144 AAACTTACATTTCTTTTGAACGGTAAG 57.489 29.630 17.58 17.58 46.79 2.34
349 350 9.292846 GTAAAACTTACATTTCTTTTGAACGGT 57.707 29.630 0.00 0.00 38.30 4.83
462 483 3.791973 TTTTCCAACACACGCTGAATT 57.208 38.095 0.00 0.00 0.00 2.17
463 484 4.050553 CAATTTTCCAACACACGCTGAAT 58.949 39.130 0.00 0.00 0.00 2.57
469 490 6.462647 GTGTTAAACAATTTTCCAACACACG 58.537 36.000 13.82 0.00 40.67 4.49
470 491 6.089685 ACGTGTTAAACAATTTTCCAACACAC 59.910 34.615 16.77 0.00 40.84 3.82
483 504 8.928270 ACATTTTTGGAATACGTGTTAAACAA 57.072 26.923 0.00 1.75 0.00 2.83
667 688 7.445900 ACACATTGTACATTTCTCGTATACG 57.554 36.000 19.23 19.23 41.45 3.06
695 716 8.719648 TGCATTTCAAAACATGTCCAATTATTC 58.280 29.630 0.00 0.00 0.00 1.75
698 719 7.714377 ACTTGCATTTCAAAACATGTCCAATTA 59.286 29.630 0.00 0.00 33.65 1.40
738 764 4.758165 TGTATCTTTCACCGGTTTTCTTCC 59.242 41.667 2.97 0.00 0.00 3.46
739 765 5.934935 TGTATCTTTCACCGGTTTTCTTC 57.065 39.130 2.97 0.00 0.00 2.87
776 805 8.968242 GTTCTCATTTTTACTTTTTCTTCGCAT 58.032 29.630 0.00 0.00 0.00 4.73
778 807 7.375017 TCGTTCTCATTTTTACTTTTTCTTCGC 59.625 33.333 0.00 0.00 0.00 4.70
814 843 5.988092 TCTTTCGGTTTTGTACGGTTATTG 58.012 37.500 0.00 0.00 0.00 1.90
822 851 8.677871 TTTCTTTTTCTCTTTCGGTTTTGTAC 57.322 30.769 0.00 0.00 0.00 2.90
823 852 9.694137 TTTTTCTTTTTCTCTTTCGGTTTTGTA 57.306 25.926 0.00 0.00 0.00 2.41
857 887 2.158900 CCAATACTGTAGCTCCCACTGG 60.159 54.545 0.00 0.00 0.00 4.00
858 888 2.158900 CCCAATACTGTAGCTCCCACTG 60.159 54.545 0.00 0.00 0.00 3.66
875 905 2.349755 GCTAGTGGAACGGCCCAA 59.650 61.111 0.00 0.00 45.86 4.12
883 913 1.375908 CTGCGCAAGGCTAGTGGAA 60.376 57.895 13.05 0.00 44.05 3.53
1095 1128 1.300697 GACGACAAGGAGCACCGTT 60.301 57.895 0.00 0.00 41.83 4.44
1198 1231 7.908601 GGAAAAACAGTACTAACAGACACAAAG 59.091 37.037 0.00 0.00 0.00 2.77
1210 1243 2.369532 AGTGCGGGGAAAAACAGTACTA 59.630 45.455 0.00 0.00 0.00 1.82
1218 1251 2.359531 CACAAACTAGTGCGGGGAAAAA 59.640 45.455 0.00 0.00 32.04 1.94
1238 1271 0.869730 GAAAACCGAAGCCTAACGCA 59.130 50.000 0.00 0.00 41.38 5.24
1350 1383 4.574674 TTCATCCTGGTCTACTTTGCAT 57.425 40.909 0.00 0.00 0.00 3.96
1390 1423 6.640907 GCACCAACCTTTAGTTTCAACAATAG 59.359 38.462 0.00 0.00 36.18 1.73
1392 1425 5.105146 TGCACCAACCTTTAGTTTCAACAAT 60.105 36.000 0.00 0.00 36.18 2.71
1416 1482 3.258372 TCGAGATGGTTTGTCTAGCAACT 59.742 43.478 0.00 0.00 36.72 3.16
1532 1603 2.036346 ACCAGGCATTTGAGCTTTTCAC 59.964 45.455 0.00 0.00 34.94 3.18
1547 1618 3.189287 CAGAAATACACTTCACACCAGGC 59.811 47.826 0.00 0.00 0.00 4.85
1596 1667 4.611943 ACTGAGCATTACGTAGCACTATG 58.388 43.478 9.22 4.95 0.00 2.23
1708 1780 9.807649 GCACATGAAGTAATTTTGGATTTCTAT 57.192 29.630 0.00 0.00 0.00 1.98
1779 1851 5.505181 AACTCCAGTTCAGTACCATGAAT 57.495 39.130 0.00 0.00 41.05 2.57
1781 1853 4.974645 AAACTCCAGTTCAGTACCATGA 57.025 40.909 0.00 0.00 37.25 3.07
1782 1854 6.710744 AGTTAAAACTCCAGTTCAGTACCATG 59.289 38.462 0.00 0.00 37.25 3.66
1783 1855 6.710744 CAGTTAAAACTCCAGTTCAGTACCAT 59.289 38.462 0.00 0.00 37.08 3.55
1784 1856 6.053005 CAGTTAAAACTCCAGTTCAGTACCA 58.947 40.000 0.00 0.00 37.08 3.25
1785 1857 6.285990 TCAGTTAAAACTCCAGTTCAGTACC 58.714 40.000 0.00 0.00 37.08 3.34
1786 1858 7.441458 ACATCAGTTAAAACTCCAGTTCAGTAC 59.559 37.037 0.00 0.00 37.08 2.73
1787 1859 7.506114 ACATCAGTTAAAACTCCAGTTCAGTA 58.494 34.615 0.00 0.00 37.08 2.74
1788 1860 6.357367 ACATCAGTTAAAACTCCAGTTCAGT 58.643 36.000 0.00 0.00 37.08 3.41
1802 1888 2.037902 TCGGCACCTGAACATCAGTTAA 59.962 45.455 6.62 0.00 42.80 2.01
1839 1925 5.468746 GCATGATAACCGTAGCCATTAGAAA 59.531 40.000 0.00 0.00 0.00 2.52
1931 2021 7.536855 ACTTAGTAAACAGAGTAGGAATCACG 58.463 38.462 0.00 0.00 0.00 4.35
1959 2049 8.421002 ACCAATTTACAAACAATTAGAGCAACT 58.579 29.630 0.00 0.00 0.00 3.16
2002 2092 5.878116 TCTACCAAATTCCAACTTCATACCG 59.122 40.000 0.00 0.00 0.00 4.02
2004 2094 8.793592 AGTTTCTACCAAATTCCAACTTCATAC 58.206 33.333 0.00 0.00 0.00 2.39
2024 2114 1.899814 TGGCTGACGATGGTAGTTTCT 59.100 47.619 0.00 0.00 0.00 2.52
2128 2218 3.499918 CGCTGTTGAGAAGACATCCTTTT 59.500 43.478 0.00 0.00 34.68 2.27
2149 2239 4.449068 AGAGACATTCACAAAACAGTAGCG 59.551 41.667 0.00 0.00 0.00 4.26
2217 2307 8.766994 AATTAAGCCATATCACCATTGTAGTT 57.233 30.769 0.00 0.00 0.00 2.24
2272 2362 7.710907 TGAACAAAGCGCTATATCTCTGTTTAT 59.289 33.333 12.05 0.00 0.00 1.40
2319 2409 3.243907 GGACCGCAAAGCATATAGAGAGT 60.244 47.826 0.00 0.00 0.00 3.24
2394 2484 4.871993 CATCTGCACCTAGATGTTTGAC 57.128 45.455 7.43 0.00 45.70 3.18
2501 2591 6.890268 GGACATTTGACCCTAAAATAAGGACT 59.110 38.462 0.00 0.00 39.15 3.85
2580 2677 7.436118 AGAAAACATGTATGTGCACTGAATTT 58.564 30.769 19.41 13.10 41.61 1.82
3279 3378 0.320683 TCGCACCAGACCATGAAGTG 60.321 55.000 0.00 0.00 0.00 3.16
3345 3444 9.717942 GTAGCTAATGGAGTATCTGAATTGAAT 57.282 33.333 0.00 0.00 33.73 2.57
3382 3481 8.445275 TTTCTTATGAAAACAGCTACAAGTCA 57.555 30.769 1.49 0.00 39.02 3.41
3402 3502 8.181904 TGAACAGAAAGGATGCTATTTTTCTT 57.818 30.769 0.00 0.00 37.68 2.52
3403 3503 7.765695 TGAACAGAAAGGATGCTATTTTTCT 57.234 32.000 0.00 0.00 39.69 2.52
3433 3539 8.894768 AATGATAGTCCACTAAAATGTCTAGC 57.105 34.615 0.00 0.00 31.39 3.42
3692 3798 8.620116 TTTGTGTCAAATGAGAATGTCTGATA 57.380 30.769 0.00 0.00 0.00 2.15
3793 4202 9.466497 AAATAAATGAGCTTCAGACTCCAAATA 57.534 29.630 0.00 0.00 32.98 1.40
3796 4205 6.942005 TGAAATAAATGAGCTTCAGACTCCAA 59.058 34.615 0.00 0.00 32.98 3.53
3834 4243 6.038997 ACCTGTAGAATATAATTCGGAGGC 57.961 41.667 11.45 0.00 0.00 4.70
3865 4274 2.159379 GCCGTGAATCAGATTTTGGGAC 60.159 50.000 0.00 0.00 0.00 4.46
4305 4714 8.993121 GTTTTCTCTCTGTTGAGATACATGAAA 58.007 33.333 0.00 0.00 46.93 2.69
4404 4813 1.553248 CGTAGAAACATCCCCACCTCA 59.447 52.381 0.00 0.00 0.00 3.86
4689 5098 6.469782 AACACATCACTTTCCACTGAAATT 57.530 33.333 0.00 0.00 39.65 1.82
4989 5744 2.002586 CTCTTAGATGCCACAACACCG 58.997 52.381 0.00 0.00 0.00 4.94
5020 5775 3.055385 TGCACTAAACTGGGTCCATCTAC 60.055 47.826 0.00 0.00 0.00 2.59
5056 5811 5.104693 TGAAGACTTTACTTGGACTCCACAA 60.105 40.000 0.00 0.00 30.78 3.33
5117 5875 7.336931 TGGAAACTATTACAAGATTGCTCCTTC 59.663 37.037 0.00 0.00 0.00 3.46
5347 6123 1.571955 TCCAGCTGGCTGTTAGATGA 58.428 50.000 28.91 3.28 42.15 2.92
5533 6309 1.871418 TCCACCAATCCTCTCCTGAG 58.129 55.000 0.00 0.00 39.92 3.35
5585 6361 0.175989 GGACAGCTTAGGACCTTCCG 59.824 60.000 0.00 0.00 42.75 4.30
5663 6442 4.857037 CAGAAGTCATGTGCATGTGATTTG 59.143 41.667 13.95 2.12 39.72 2.32
5789 6570 7.403231 TCATAAAAGGATTCCTCTGTCCTAAGT 59.597 37.037 5.48 0.00 43.94 2.24
6044 6825 8.094798 TCTATGGTTAACTTTTGCTGTACTTG 57.905 34.615 5.42 0.00 0.00 3.16
6123 6909 2.462456 TCACAGGCAAGCTAGAACAG 57.538 50.000 0.00 0.00 0.00 3.16
6267 7053 5.356882 TGAGCAGCAACTACAACATAAAC 57.643 39.130 0.00 0.00 0.00 2.01
6330 7141 8.494433 ACTCAAATGGTTCTAGGATATGCTAAA 58.506 33.333 5.40 1.07 0.00 1.85
6341 7160 7.496529 TCAAAGTTCACTCAAATGGTTCTAG 57.503 36.000 0.00 0.00 0.00 2.43
6379 7198 7.363355 GCTCCAGTATATGTGATATGTAGCTGT 60.363 40.741 0.00 0.00 0.00 4.40
6390 7209 5.941788 TCACTAGAGCTCCAGTATATGTGA 58.058 41.667 14.70 11.67 0.00 3.58
6391 7210 6.619744 CATCACTAGAGCTCCAGTATATGTG 58.380 44.000 14.70 9.78 0.00 3.21
6392 7211 5.184864 GCATCACTAGAGCTCCAGTATATGT 59.815 44.000 24.49 7.84 0.00 2.29
6393 7212 5.394005 GGCATCACTAGAGCTCCAGTATATG 60.394 48.000 21.97 21.97 0.00 1.78
6394 7213 4.709397 GGCATCACTAGAGCTCCAGTATAT 59.291 45.833 14.70 8.70 0.00 0.86
6427 7289 6.273071 CGTCATGGAGTATGAGTGTGATTTA 58.727 40.000 0.00 0.00 46.09 1.40
6515 7377 0.687354 CTTGCCGGCCTCCATATACT 59.313 55.000 26.77 0.00 0.00 2.12
6516 7378 0.396811 ACTTGCCGGCCTCCATATAC 59.603 55.000 26.77 0.00 0.00 1.47
6517 7379 0.396435 CACTTGCCGGCCTCCATATA 59.604 55.000 26.77 0.00 0.00 0.86
6518 7380 1.149174 CACTTGCCGGCCTCCATAT 59.851 57.895 26.77 0.00 0.00 1.78
6519 7381 2.589540 CACTTGCCGGCCTCCATA 59.410 61.111 26.77 0.00 0.00 2.74
6537 7399 7.600375 ACTGATACATGTAGAGTTGTTTCACTG 59.400 37.037 11.91 0.29 32.71 3.66
6646 7508 3.287222 GCATATAACAACTTCCAGGCCA 58.713 45.455 5.01 0.00 0.00 5.36
6670 7532 3.577389 CCTAAAGGTGCCTTCAGGG 57.423 57.895 11.59 7.19 37.72 4.45
6750 7612 8.451687 ACACATCATTTGTAACGATGATTTTG 57.548 30.769 5.67 4.69 40.14 2.44
6752 7614 8.946085 AGTACACATCATTTGTAACGATGATTT 58.054 29.630 5.67 0.00 40.14 2.17
6818 7680 9.425893 CGTTCATCACATAATCTGTTTCATTAC 57.574 33.333 0.00 0.00 35.29 1.89
6823 7685 6.961554 GGTTCGTTCATCACATAATCTGTTTC 59.038 38.462 0.00 0.00 35.29 2.78
6834 7697 1.542328 CCACTGGGTTCGTTCATCACA 60.542 52.381 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.