Multiple sequence alignment - TraesCS7B01G205600

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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 TraesCS7B01G205600 chr7B 100.000 4386 0 0 1 4386 376429982 376434367 0.000000e+00 8100.0
1 TraesCS7B01G205600 chr7B 84.000 225 31 4 1605 1825 455272016 455271793 1.240000e-50 211.0
2 TraesCS7B01G205600 chr7A 91.961 2973 114 54 836 3750 430239977 430242882 0.000000e+00 4050.0
3 TraesCS7B01G205600 chr7A 90.642 748 53 9 12 755 430239226 430239960 0.000000e+00 977.0
4 TraesCS7B01G205600 chr7A 83.556 225 32 4 1605 1825 489163240 489163463 5.750000e-49 206.0
5 TraesCS7B01G205600 chr7D 93.442 1540 62 12 2300 3816 382256811 382258334 0.000000e+00 2248.0
6 TraesCS7B01G205600 chr7D 90.650 877 41 22 1446 2299 382255902 382256760 0.000000e+00 1127.0
7 TraesCS7B01G205600 chr7D 88.058 762 32 16 697 1413 382255093 382255840 0.000000e+00 848.0
8 TraesCS7B01G205600 chr7D 95.278 360 12 4 3833 4187 517345662 517345303 2.290000e-157 566.0
9 TraesCS7B01G205600 chr7D 80.202 692 96 27 20 680 382254345 382255026 8.530000e-132 481.0
10 TraesCS7B01G205600 chr7D 84.000 225 31 4 1605 1825 438368655 438368878 1.240000e-50 211.0
11 TraesCS7B01G205600 chr7D 88.281 128 13 2 1582 1708 215096309 215096183 7.600000e-33 152.0
12 TraesCS7B01G205600 chr3A 97.127 557 3 1 3830 4386 101611871 101611328 0.000000e+00 928.0
13 TraesCS7B01G205600 chr5B 96.948 557 3 2 3831 4386 71789697 71789154 0.000000e+00 922.0
14 TraesCS7B01G205600 chr1B 96.757 555 5 1 3832 4386 418826552 418827093 0.000000e+00 913.0
15 TraesCS7B01G205600 chr5A 96.577 555 6 1 3832 4386 364373196 364373737 0.000000e+00 907.0
16 TraesCS7B01G205600 chr3B 96.558 552 6 2 3835 4386 34683928 34684466 0.000000e+00 902.0
17 TraesCS7B01G205600 chr3B 92.391 184 1 1 4203 4386 669434469 669434299 2.620000e-62 250.0
18 TraesCS7B01G205600 chr4B 96.370 551 7 1 3836 4386 5701913 5701376 0.000000e+00 894.0
19 TraesCS7B01G205600 chr4B 77.246 167 29 9 1015 1178 67771414 67771574 6.040000e-14 89.8
20 TraesCS7B01G205600 chr6A 94.585 554 9 5 3833 4386 604562939 604562407 0.000000e+00 837.0
21 TraesCS7B01G205600 chr2D 95.278 360 12 4 3833 4187 316326408 316326049 2.290000e-157 566.0
22 TraesCS7B01G205600 chr2D 88.048 251 25 4 1579 1825 568801800 568802049 4.290000e-75 292.0
23 TraesCS7B01G205600 chr2D 80.423 189 25 3 1004 1180 568801320 568801508 2.750000e-27 134.0
24 TraesCS7B01G205600 chr2D 75.221 226 43 13 1606 1826 398087116 398086899 1.300000e-15 95.3
25 TraesCS7B01G205600 chr2A 87.649 251 26 4 1579 1825 708059137 708059386 2.000000e-73 287.0
26 TraesCS7B01G205600 chr2A 99.237 131 1 0 4256 4386 675099276 675099406 2.040000e-58 237.0
27 TraesCS7B01G205600 chr2B 88.115 244 24 4 1579 1818 681409271 681409513 7.180000e-73 285.0
28 TraesCS7B01G205600 chr2B 82.873 181 26 4 1004 1180 681408801 681408980 1.630000e-34 158.0
29 TraesCS7B01G205600 chr1D 85.000 160 15 5 2996 3150 2514789 2514944 2.110000e-33 154.0
30 TraesCS7B01G205600 chr4D 77.108 166 31 7 1018 1181 46293024 46292864 6.040000e-14 89.8
31 TraesCS7B01G205600 chr4A 77.108 166 31 7 1015 1178 552698531 552698691 6.040000e-14 89.8


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 TraesCS7B01G205600 chr7B 376429982 376434367 4385 False 8100.0 8100 100.0000 1 4386 1 chr7B.!!$F1 4385
1 TraesCS7B01G205600 chr7A 430239226 430242882 3656 False 2513.5 4050 91.3015 12 3750 2 chr7A.!!$F2 3738
2 TraesCS7B01G205600 chr7D 382254345 382258334 3989 False 1176.0 2248 88.0880 20 3816 4 chr7D.!!$F2 3796
3 TraesCS7B01G205600 chr3A 101611328 101611871 543 True 928.0 928 97.1270 3830 4386 1 chr3A.!!$R1 556
4 TraesCS7B01G205600 chr5B 71789154 71789697 543 True 922.0 922 96.9480 3831 4386 1 chr5B.!!$R1 555
5 TraesCS7B01G205600 chr1B 418826552 418827093 541 False 913.0 913 96.7570 3832 4386 1 chr1B.!!$F1 554
6 TraesCS7B01G205600 chr5A 364373196 364373737 541 False 907.0 907 96.5770 3832 4386 1 chr5A.!!$F1 554
7 TraesCS7B01G205600 chr3B 34683928 34684466 538 False 902.0 902 96.5580 3835 4386 1 chr3B.!!$F1 551
8 TraesCS7B01G205600 chr4B 5701376 5701913 537 True 894.0 894 96.3700 3836 4386 1 chr4B.!!$R1 550
9 TraesCS7B01G205600 chr6A 604562407 604562939 532 True 837.0 837 94.5850 3833 4386 1 chr6A.!!$R1 553
10 TraesCS7B01G205600 chr2D 568801320 568802049 729 False 213.0 292 84.2355 1004 1825 2 chr2D.!!$F1 821
11 TraesCS7B01G205600 chr2B 681408801 681409513 712 False 221.5 285 85.4940 1004 1818 2 chr2B.!!$F1 814

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
128 129 0.039074 GTGGGTGTCGTGTCTCTCTG 60.039 60.0 0.00 0.0 0.0 3.35 F
129 130 0.179001 TGGGTGTCGTGTCTCTCTGA 60.179 55.0 0.00 0.0 0.0 3.27 F
576 602 0.321564 TGGCAAGTTGATGGAGTCCG 60.322 55.0 7.16 0.0 0.0 4.79 F
1239 1358 0.459899 TCAACGTCACTGCTGTCTGT 59.540 50.0 0.00 0.0 0.0 3.41 F
2880 3241 0.034767 CAATGGGAGCCTTCTCAGCA 60.035 55.0 0.00 0.0 37.2 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1244 1363 0.322546 ATGAACGAAGGGAGGTTGCC 60.323 55.0 0.0 0.0 0.0 4.52 R
1291 1426 0.375454 TGCACGAACAAGAACCAACG 59.625 50.0 0.0 0.0 0.0 4.10 R
1952 2247 0.804989 GCGAACCAGATGAACCCAAG 59.195 55.0 0.0 0.0 0.0 3.61 R
3124 3504 1.111116 TGTAGGCGTCGATAAGGGGG 61.111 60.0 0.0 0.0 0.0 5.40 R
3818 4205 0.533032 GCGAAAGTCCTCTGGCTAGT 59.467 55.0 0.0 0.0 0.0 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
54 55 1.420138 CGGGTTTGATGGCCTAGGTAT 59.580 52.381 11.31 5.48 0.00 2.73
57 58 3.138468 GGGTTTGATGGCCTAGGTATCTT 59.862 47.826 21.32 7.87 0.00 2.40
77 78 3.250323 CGTGGCACGAGCGAGATG 61.250 66.667 34.85 1.03 46.05 2.90
128 129 0.039074 GTGGGTGTCGTGTCTCTCTG 60.039 60.000 0.00 0.00 0.00 3.35
129 130 0.179001 TGGGTGTCGTGTCTCTCTGA 60.179 55.000 0.00 0.00 0.00 3.27
130 131 0.959553 GGGTGTCGTGTCTCTCTGAA 59.040 55.000 0.00 0.00 0.00 3.02
163 165 1.318380 CCCCTCCCCATACCAGAGT 59.682 63.158 0.00 0.00 0.00 3.24
165 167 1.596496 CCCTCCCCATACCAGAGTTT 58.404 55.000 0.00 0.00 0.00 2.66
190 192 5.163343 CCGATAGAAACCCAAGTCCATCTTA 60.163 44.000 0.00 0.00 34.21 2.10
202 204 3.013921 GTCCATCTTATTGGTTTCGGCA 58.986 45.455 0.00 0.00 38.01 5.69
212 214 1.286880 GTTTCGGCAGCAGCAATGT 59.713 52.632 2.65 0.00 44.61 2.71
261 287 3.864003 GCATCGTGGAGTTTAGTACCTTC 59.136 47.826 0.00 0.00 0.00 3.46
271 297 3.334583 TTAGTACCTTCAGGCAAGCTG 57.665 47.619 0.00 0.00 39.32 4.24
281 307 0.900647 AGGCAAGCTGGACTCGTAGT 60.901 55.000 0.00 0.00 0.00 2.73
355 381 1.002430 ACAAGTGACTGCATCGTCCAT 59.998 47.619 3.85 0.00 32.97 3.41
359 385 3.461061 AGTGACTGCATCGTCCATATTG 58.539 45.455 3.85 0.00 32.97 1.90
422 448 2.204059 AGCAAGAGGGCAGAGGGT 60.204 61.111 0.00 0.00 35.83 4.34
464 490 1.841663 GCGGTTGTGCAACGATGTCT 61.842 55.000 8.70 0.00 42.39 3.41
519 545 2.835895 GGTGGCCACCGGTGTTTT 60.836 61.111 38.35 0.00 42.29 2.43
576 602 0.321564 TGGCAAGTTGATGGAGTCCG 60.322 55.000 7.16 0.00 0.00 4.79
603 629 4.823157 TGCATATCTTGTGCATTGCTTTT 58.177 34.783 10.49 0.00 46.76 2.27
610 636 2.969990 TGTGCATTGCTTTTGTGTTGT 58.030 38.095 10.49 0.00 0.00 3.32
615 641 4.694509 TGCATTGCTTTTGTGTTGTTTTCT 59.305 33.333 10.49 0.00 0.00 2.52
625 651 7.401484 TTTGTGTTGTTTTCTTTGTTGTCTC 57.599 32.000 0.00 0.00 0.00 3.36
629 655 7.328249 TGTGTTGTTTTCTTTGTTGTCTCATTC 59.672 33.333 0.00 0.00 0.00 2.67
654 680 9.268268 TCTTTTTCTTTAATCTACTTTGCGAGA 57.732 29.630 0.00 0.00 0.00 4.04
785 869 3.026694 GGAGGATGTCCCAAAAATGAGG 58.973 50.000 0.00 0.00 39.88 3.86
823 907 3.907894 GGTTTCAAACCGTAAGCATCA 57.092 42.857 2.78 0.00 42.62 3.07
943 1044 2.235898 CAAAACTCTCTCTCCCTCCCTG 59.764 54.545 0.00 0.00 0.00 4.45
991 1096 0.801067 GTAGCAGTGTAGCGTTCCGG 60.801 60.000 0.00 0.00 40.15 5.14
994 1099 1.585006 CAGTGTAGCGTTCCGGTCT 59.415 57.895 0.00 0.00 38.83 3.85
1222 1341 2.130272 ACGTGCCTACTCATCTCTCA 57.870 50.000 0.00 0.00 0.00 3.27
1236 1355 1.001268 TCTCTCAACGTCACTGCTGTC 60.001 52.381 0.00 0.00 0.00 3.51
1237 1356 1.000827 CTCTCAACGTCACTGCTGTCT 60.001 52.381 0.00 0.00 0.00 3.41
1238 1357 1.135046 CTCAACGTCACTGCTGTCTG 58.865 55.000 0.00 0.00 0.00 3.51
1239 1358 0.459899 TCAACGTCACTGCTGTCTGT 59.540 50.000 0.00 0.00 0.00 3.41
1244 1363 0.855349 GTCACTGCTGTCTGTTCGTG 59.145 55.000 0.00 0.00 0.00 4.35
1252 1371 0.531974 TGTCTGTTCGTGGCAACCTC 60.532 55.000 0.00 0.00 0.00 3.85
1253 1372 1.070786 TCTGTTCGTGGCAACCTCC 59.929 57.895 0.00 0.00 0.00 4.30
1340 1483 2.106683 GCGCTGGCGACCAACTTAT 61.107 57.895 19.31 0.00 42.83 1.73
1393 1538 5.256474 TCTTCATGGAAAGGAAGGTTGATC 58.744 41.667 0.00 0.00 40.65 2.92
1398 1543 5.429681 TGGAAAGGAAGGTTGATCGATTA 57.570 39.130 0.00 0.00 0.00 1.75
1465 1653 5.217393 GTGTGTTAGACTGACGTGATAACA 58.783 41.667 0.00 0.00 33.18 2.41
1494 1770 5.200454 CACCTCGCTGAAATCATATTTTCG 58.800 41.667 0.00 0.00 38.23 3.46
1495 1771 4.876107 ACCTCGCTGAAATCATATTTTCGT 59.124 37.500 0.00 0.00 38.23 3.85
1543 1829 5.010922 ACAGATTGGTTGCATGCTAAAAGAA 59.989 36.000 20.33 0.00 0.00 2.52
1544 1830 5.927689 CAGATTGGTTGCATGCTAAAAGAAA 59.072 36.000 20.33 0.00 0.00 2.52
1545 1831 6.424509 CAGATTGGTTGCATGCTAAAAGAAAA 59.575 34.615 20.33 0.00 0.00 2.29
1551 1837 7.066766 TGGTTGCATGCTAAAAGAAAATGTTTT 59.933 29.630 20.33 0.00 0.00 2.43
1565 1851 7.308435 AGAAAATGTTTTGATGGATTCGTCTC 58.692 34.615 0.00 0.00 0.00 3.36
1857 2152 3.563224 ACCACCAGCAGCAGCAGA 61.563 61.111 3.17 0.00 45.49 4.26
1858 2153 2.281970 CCACCAGCAGCAGCAGAA 60.282 61.111 3.17 0.00 45.49 3.02
1859 2154 2.333417 CCACCAGCAGCAGCAGAAG 61.333 63.158 3.17 0.00 45.49 2.85
1862 2157 3.441290 CAGCAGCAGCAGAAGGGC 61.441 66.667 3.17 0.00 45.49 5.19
1865 2160 4.711949 CAGCAGCAGAAGGGCGGT 62.712 66.667 0.00 0.00 39.27 5.68
1866 2161 4.711949 AGCAGCAGAAGGGCGGTG 62.712 66.667 0.00 0.00 39.27 4.94
2031 2326 3.891366 GGAATTGAGGAGGAGAGAGAGAG 59.109 52.174 0.00 0.00 0.00 3.20
2032 2327 4.386312 GGAATTGAGGAGGAGAGAGAGAGA 60.386 50.000 0.00 0.00 0.00 3.10
2042 2337 5.501156 AGGAGAGAGAGAGAAGAGAGTTTC 58.499 45.833 0.00 0.00 0.00 2.78
2104 2407 7.962917 CAAGTGAAAATTGCACAGTTTTTAGT 58.037 30.769 6.89 2.46 34.12 2.24
2144 2449 8.428186 AAATGCATAATTTTGTGGCTAAGATG 57.572 30.769 0.00 0.00 34.72 2.90
2159 2464 5.482175 GGCTAAGATGGATATCACTACCTGT 59.518 44.000 4.83 0.00 35.70 4.00
2160 2465 6.014156 GGCTAAGATGGATATCACTACCTGTT 60.014 42.308 4.83 0.00 35.70 3.16
2419 2780 9.812347 ATTTTAGAATGAGGCATATGTATTCCA 57.188 29.630 4.29 0.00 0.00 3.53
2465 2826 2.028766 ATCATACGCGTCGTCGTCGT 62.029 55.000 18.63 21.61 45.41 4.34
2466 2827 2.020559 ATACGCGTCGTCGTCGTC 59.979 61.111 18.63 5.26 43.74 4.20
2467 2828 3.741063 ATACGCGTCGTCGTCGTCG 62.741 63.158 18.63 15.68 46.99 5.12
2474 2835 1.119015 GTCGTCGTCGTCGTCATGTC 61.119 60.000 11.41 0.00 38.33 3.06
2640 3001 3.005050 TGATCGTTCCAGTGTTTACGTCT 59.995 43.478 0.00 0.00 35.63 4.18
2647 3008 2.210116 CAGTGTTTACGTCTGGCAACT 58.790 47.619 0.00 0.00 37.61 3.16
2662 3023 7.201444 CGTCTGGCAACTAACTAACTAAATGAG 60.201 40.741 0.00 0.00 37.61 2.90
2665 3026 8.718102 TGGCAACTAACTAACTAAATGAGATC 57.282 34.615 0.00 0.00 37.61 2.75
2733 3094 4.174009 TCGCATGTGCTAGTTCTTTACTC 58.826 43.478 0.00 0.00 39.32 2.59
2834 3195 4.640201 TCATAAAGTAACCAGATTGCTGCC 59.360 41.667 0.00 0.00 40.91 4.85
2856 3217 4.747108 CCGAGATTGGCTACTGAATTAGTG 59.253 45.833 0.00 0.00 40.65 2.74
2867 3228 7.041098 GGCTACTGAATTAGTGTAATCAATGGG 60.041 40.741 0.00 0.00 40.65 4.00
2880 3241 0.034767 CAATGGGAGCCTTCTCAGCA 60.035 55.000 0.00 0.00 37.20 4.41
2959 3332 9.891828 GTTTCAATTGTTACATACATGAACTCA 57.108 29.630 5.13 0.00 36.17 3.41
3096 3476 0.883833 ACATTTTTCAGCGAGCTGGG 59.116 50.000 22.93 9.75 43.75 4.45
3107 3487 3.672295 GAGCTGGGCCTTCCGACTG 62.672 68.421 4.53 0.00 38.76 3.51
3150 3530 0.887836 ATCGACGCCTACATCGCCTA 60.888 55.000 0.00 0.00 38.24 3.93
3205 3585 2.058595 GTCCTGCTTCTCCGGCCTA 61.059 63.158 0.00 0.00 0.00 3.93
3413 3793 9.702494 TCTTGATATGAGATTATTGTGCTACTG 57.298 33.333 0.00 0.00 0.00 2.74
3414 3794 9.486497 CTTGATATGAGATTATTGTGCTACTGT 57.514 33.333 0.00 0.00 0.00 3.55
3457 3837 8.910944 TGGTGACTAGTAAGTAATTAGATGACC 58.089 37.037 0.00 0.00 35.56 4.02
3737 4124 4.554973 GTGATAAATTGTTCTTCAGTGCGC 59.445 41.667 0.00 0.00 0.00 6.09
3750 4137 2.223144 TCAGTGCGCTAAACATGTTGTC 59.777 45.455 12.82 3.52 0.00 3.18
3770 4157 2.172505 TCAATATGAAGCATCCCCACGT 59.827 45.455 0.00 0.00 0.00 4.49
3773 4160 2.260844 ATGAAGCATCCCCACGTATG 57.739 50.000 0.00 0.00 0.00 2.39
3779 4166 0.756294 CATCCCCACGTATGTAGGCA 59.244 55.000 0.00 0.00 0.00 4.75
3816 4203 9.627123 TTCAAATACTATCACTTAATTCCCCAG 57.373 33.333 0.00 0.00 0.00 4.45
3817 4204 8.998814 TCAAATACTATCACTTAATTCCCCAGA 58.001 33.333 0.00 0.00 0.00 3.86
3818 4205 9.627123 CAAATACTATCACTTAATTCCCCAGAA 57.373 33.333 0.00 0.00 36.15 3.02
3819 4206 9.628500 AAATACTATCACTTAATTCCCCAGAAC 57.372 33.333 0.00 0.00 33.97 3.01
3820 4207 6.893020 ACTATCACTTAATTCCCCAGAACT 57.107 37.500 0.00 0.00 33.97 3.01
3821 4208 7.989947 ACTATCACTTAATTCCCCAGAACTA 57.010 36.000 0.00 0.00 33.97 2.24
3822 4209 8.024145 ACTATCACTTAATTCCCCAGAACTAG 57.976 38.462 0.00 0.00 33.97 2.57
3823 4210 5.099042 TCACTTAATTCCCCAGAACTAGC 57.901 43.478 0.00 0.00 33.97 3.42
3824 4211 4.080526 TCACTTAATTCCCCAGAACTAGCC 60.081 45.833 0.00 0.00 33.97 3.93
3825 4212 3.850173 ACTTAATTCCCCAGAACTAGCCA 59.150 43.478 0.00 0.00 33.97 4.75
3826 4213 4.080299 ACTTAATTCCCCAGAACTAGCCAG 60.080 45.833 0.00 0.00 33.97 4.85
3827 4214 2.270434 ATTCCCCAGAACTAGCCAGA 57.730 50.000 0.00 0.00 33.97 3.86
3828 4215 1.573108 TTCCCCAGAACTAGCCAGAG 58.427 55.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.302431 CCACTGCCATTGTCGACCA 60.302 57.895 14.12 1.38 0.00 4.02
2 3 2.040544 CCCACTGCCATTGTCGACC 61.041 63.158 14.12 0.00 0.00 4.79
3 4 2.690778 GCCCACTGCCATTGTCGAC 61.691 63.158 9.11 9.11 0.00 4.20
34 35 0.834612 TACCTAGGCCATCAAACCCG 59.165 55.000 9.30 0.00 0.00 5.28
54 55 2.355837 GCTCGTGCCACGTCAAGA 60.356 61.111 17.83 0.00 43.14 3.02
57 58 4.700365 CTCGCTCGTGCCACGTCA 62.700 66.667 17.83 0.00 43.14 4.35
77 78 1.809209 GACTGCTTCGAGGCTCAGC 60.809 63.158 20.92 17.40 0.00 4.26
150 152 1.200519 TCGGAAACTCTGGTATGGGG 58.799 55.000 0.00 0.00 0.00 4.96
163 165 3.328343 TGGACTTGGGTTTCTATCGGAAA 59.672 43.478 0.00 0.00 41.11 3.13
165 167 2.542550 TGGACTTGGGTTTCTATCGGA 58.457 47.619 0.00 0.00 0.00 4.55
190 192 1.462731 TTGCTGCTGCCGAAACCAAT 61.463 50.000 13.47 0.00 38.71 3.16
202 204 2.892852 ACAATACCACAACATTGCTGCT 59.107 40.909 0.00 0.00 35.91 4.24
212 214 4.141287 CCAAGAGGTTGACAATACCACAA 58.859 43.478 0.00 0.00 38.16 3.33
261 287 0.459237 CTACGAGTCCAGCTTGCCTG 60.459 60.000 0.00 0.00 41.41 4.85
281 307 2.742053 CCAAAGCCGAAGAATCTTCGAA 59.258 45.455 37.50 0.00 43.97 3.71
295 321 1.620822 AATCACCTCACACCAAAGCC 58.379 50.000 0.00 0.00 0.00 4.35
355 381 0.546122 ATCAGCAAGGGCCGACAATA 59.454 50.000 0.00 0.00 42.56 1.90
359 385 0.392461 TACAATCAGCAAGGGCCGAC 60.392 55.000 0.00 0.00 42.56 4.79
422 448 1.593196 CAAACTGTCGCCAAAGAGGA 58.407 50.000 0.00 0.00 41.22 3.71
446 472 0.110688 CAGACATCGTTGCACAACCG 60.111 55.000 7.88 3.95 38.03 4.44
464 490 3.262420 GCATCTCGTTAAGAAAGCTCCA 58.738 45.455 0.00 0.00 37.61 3.86
519 545 1.830477 GATTAGCCCAACCCATGCAAA 59.170 47.619 0.00 0.00 0.00 3.68
524 550 3.099141 CACAAAGATTAGCCCAACCCAT 58.901 45.455 0.00 0.00 0.00 4.00
531 557 2.223665 GCATGAGCACAAAGATTAGCCC 60.224 50.000 0.00 0.00 41.58 5.19
603 629 6.078202 TGAGACAACAAAGAAAACAACACA 57.922 33.333 0.00 0.00 0.00 3.72
610 636 9.927668 AGAAAAAGAATGAGACAACAAAGAAAA 57.072 25.926 0.00 0.00 0.00 2.29
629 655 9.535270 CTCTCGCAAAGTAGATTAAAGAAAAAG 57.465 33.333 0.00 0.00 0.00 2.27
691 775 5.504994 CCGCTTTATTTATAATGCCACACGT 60.505 40.000 12.17 0.00 39.10 4.49
693 777 5.009210 TCCCGCTTTATTTATAATGCCACAC 59.991 40.000 12.17 0.00 39.10 3.82
762 846 4.079787 CCTCATTTTTGGGACATCCTCCTA 60.080 45.833 0.00 0.00 39.30 2.94
763 847 3.309410 CCTCATTTTTGGGACATCCTCCT 60.309 47.826 0.00 0.00 39.30 3.69
784 868 2.030451 ACCGTAAGTCTTCAACGACTCC 60.030 50.000 9.06 0.00 43.14 3.85
785 869 3.279853 ACCGTAAGTCTTCAACGACTC 57.720 47.619 9.06 0.00 43.14 3.36
823 907 7.335627 TGCTACTACCACTATACTTTTGCATT 58.664 34.615 0.00 0.00 0.00 3.56
839 923 2.711542 ACAATGCAACCTGCTACTACC 58.288 47.619 0.00 0.00 45.31 3.18
943 1044 0.188342 AGAGAGGGAGAGATGGAGGC 59.812 60.000 0.00 0.00 0.00 4.70
986 1091 2.952978 GAGCTCATCTTCTAGACCGGAA 59.047 50.000 9.46 0.00 0.00 4.30
991 1096 5.010516 TGCCAATAGAGCTCATCTTCTAGAC 59.989 44.000 17.77 0.00 39.64 2.59
994 1099 5.541484 TCATGCCAATAGAGCTCATCTTCTA 59.459 40.000 17.77 0.00 39.64 2.10
1199 1318 4.141779 TGAGAGATGAGTAGGCACGTACTA 60.142 45.833 3.18 0.00 33.18 1.82
1200 1319 3.207778 GAGAGATGAGTAGGCACGTACT 58.792 50.000 2.82 2.82 35.88 2.73
1201 1320 2.943690 TGAGAGATGAGTAGGCACGTAC 59.056 50.000 0.00 0.00 0.00 3.67
1222 1341 1.571919 GAACAGACAGCAGTGACGTT 58.428 50.000 0.00 0.00 0.00 3.99
1236 1355 1.966451 GGGAGGTTGCCACGAACAG 60.966 63.158 0.00 0.00 0.00 3.16
1237 1356 1.990160 AAGGGAGGTTGCCACGAACA 61.990 55.000 0.00 0.00 0.00 3.18
1238 1357 1.228154 AAGGGAGGTTGCCACGAAC 60.228 57.895 0.00 0.00 0.00 3.95
1239 1358 1.072505 GAAGGGAGGTTGCCACGAA 59.927 57.895 0.00 0.00 0.00 3.85
1244 1363 0.322546 ATGAACGAAGGGAGGTTGCC 60.323 55.000 0.00 0.00 0.00 4.52
1252 1371 0.814010 CCGGGCTAATGAACGAAGGG 60.814 60.000 0.00 0.00 0.00 3.95
1253 1372 1.436983 GCCGGGCTAATGAACGAAGG 61.437 60.000 12.87 0.00 0.00 3.46
1280 1415 0.806492 GAACCAACGGAGCTCGATCC 60.806 60.000 7.83 0.00 42.43 3.36
1291 1426 0.375454 TGCACGAACAAGAACCAACG 59.625 50.000 0.00 0.00 0.00 4.10
1376 1521 4.301072 AATCGATCAACCTTCCTTTCCA 57.699 40.909 0.00 0.00 0.00 3.53
1413 1558 2.293122 CTCCGGATTGTTTTCACTTGCA 59.707 45.455 3.57 0.00 0.00 4.08
1415 1560 3.058224 GGTCTCCGGATTGTTTTCACTTG 60.058 47.826 3.57 0.00 0.00 3.16
1465 1653 4.002906 TGATTTCAGCGAGGTGTAGTTT 57.997 40.909 2.10 0.00 0.00 2.66
1506 1782 8.538701 TGCAACCAATCTGTCCAAATATATTTT 58.461 29.630 8.01 0.00 0.00 1.82
1510 1786 6.461370 GCATGCAACCAATCTGTCCAAATATA 60.461 38.462 14.21 0.00 0.00 0.86
1511 1787 5.682990 GCATGCAACCAATCTGTCCAAATAT 60.683 40.000 14.21 0.00 0.00 1.28
1512 1788 4.381825 GCATGCAACCAATCTGTCCAAATA 60.382 41.667 14.21 0.00 0.00 1.40
1543 1829 6.656693 AGAGAGACGAATCCATCAAAACATTT 59.343 34.615 0.00 0.00 0.00 2.32
1544 1830 6.176183 AGAGAGACGAATCCATCAAAACATT 58.824 36.000 0.00 0.00 0.00 2.71
1545 1831 5.738909 AGAGAGACGAATCCATCAAAACAT 58.261 37.500 0.00 0.00 0.00 2.71
1551 1837 3.634448 GGAGAAGAGAGACGAATCCATCA 59.366 47.826 0.00 0.00 0.00 3.07
1565 1851 1.675415 GCCTCTGCACAAGGAGAAGAG 60.675 57.143 13.50 1.19 41.98 2.85
1884 2179 2.435586 CTTGAGCTGGCACCTCGG 60.436 66.667 5.40 0.00 31.98 4.63
1946 2241 4.453480 ACCAGATGAACCCAAGAAAGAA 57.547 40.909 0.00 0.00 0.00 2.52
1947 2242 4.398319 GAACCAGATGAACCCAAGAAAGA 58.602 43.478 0.00 0.00 0.00 2.52
1952 2247 0.804989 GCGAACCAGATGAACCCAAG 59.195 55.000 0.00 0.00 0.00 3.61
2042 2337 6.978080 TGAACCGAAAATGAAAAAGGAAAGAG 59.022 34.615 0.00 0.00 0.00 2.85
2081 2381 7.431084 CGTACTAAAAACTGTGCAATTTTCACT 59.569 33.333 8.53 0.00 35.58 3.41
2179 2485 3.527533 TGCACACTTTGTAGAACGAACT 58.472 40.909 0.00 0.00 0.00 3.01
2419 2780 7.277396 ACAGTTATATAAATGGGCTAACACGT 58.723 34.615 22.83 0.00 35.75 4.49
2474 2835 4.571984 TCATACGAAATTCCAGCATGACAG 59.428 41.667 0.00 0.00 39.69 3.51
2640 3001 8.318412 TGATCTCATTTAGTTAGTTAGTTGCCA 58.682 33.333 0.00 0.00 0.00 4.92
2733 3094 9.927668 ATCAATAATTTTAAACTGTCACCTTGG 57.072 29.630 0.00 0.00 0.00 3.61
2834 3195 5.352284 ACACTAATTCAGTAGCCAATCTCG 58.648 41.667 0.00 0.00 34.98 4.04
2856 3217 4.133078 CTGAGAAGGCTCCCATTGATTAC 58.867 47.826 0.00 0.00 40.55 1.89
2867 3228 2.998316 AGGTTATGCTGAGAAGGCTC 57.002 50.000 0.00 0.00 41.67 4.70
2958 3331 4.298332 GCAAGGTTCAAATGGTAAGTGTG 58.702 43.478 0.00 0.00 0.00 3.82
2959 3332 3.320826 GGCAAGGTTCAAATGGTAAGTGT 59.679 43.478 0.00 0.00 0.00 3.55
3124 3504 1.111116 TGTAGGCGTCGATAAGGGGG 61.111 60.000 0.00 0.00 0.00 5.40
3230 3610 2.113243 AACAGGTCCCCGAAGCTCAC 62.113 60.000 0.00 0.00 0.00 3.51
3289 3669 4.450976 TGTTACTTGACATGTTGCTCAGT 58.549 39.130 0.00 0.92 0.00 3.41
3411 3791 4.202223 ACCACCACACTTCAACTAGTACAG 60.202 45.833 0.00 0.00 0.00 2.74
3412 3792 3.707611 ACCACCACACTTCAACTAGTACA 59.292 43.478 0.00 0.00 0.00 2.90
3413 3793 4.056050 CACCACCACACTTCAACTAGTAC 58.944 47.826 0.00 0.00 0.00 2.73
3414 3794 3.962063 TCACCACCACACTTCAACTAGTA 59.038 43.478 0.00 0.00 0.00 1.82
3415 3795 2.769663 TCACCACCACACTTCAACTAGT 59.230 45.455 0.00 0.00 0.00 2.57
3494 3874 1.888215 ACAGACACTGCATCAACCAG 58.112 50.000 0.00 0.00 34.37 4.00
3737 4124 9.229784 GATGCTTCATATTGACAACATGTTTAG 57.770 33.333 8.77 0.88 0.00 1.85
3750 4137 2.575532 ACGTGGGGATGCTTCATATTG 58.424 47.619 1.64 0.00 0.00 1.90
3796 4183 7.989947 AGTTCTGGGGAATTAAGTGATAGTA 57.010 36.000 0.00 0.00 33.71 1.82
3807 4194 2.507471 CTCTGGCTAGTTCTGGGGAATT 59.493 50.000 0.00 0.00 33.71 2.17
3816 4203 2.882324 CGAAAGTCCTCTGGCTAGTTC 58.118 52.381 0.00 0.00 0.00 3.01
3817 4204 1.066787 GCGAAAGTCCTCTGGCTAGTT 60.067 52.381 0.00 0.00 0.00 2.24
3818 4205 0.533032 GCGAAAGTCCTCTGGCTAGT 59.467 55.000 0.00 0.00 0.00 2.57
3819 4206 0.820871 AGCGAAAGTCCTCTGGCTAG 59.179 55.000 0.00 0.00 0.00 3.42
3820 4207 0.818296 GAGCGAAAGTCCTCTGGCTA 59.182 55.000 0.00 0.00 0.00 3.93
3821 4208 1.594310 GAGCGAAAGTCCTCTGGCT 59.406 57.895 0.00 0.00 0.00 4.75
3822 4209 1.807573 CGAGCGAAAGTCCTCTGGC 60.808 63.158 0.00 0.00 0.00 4.85
3823 4210 1.807573 GCGAGCGAAAGTCCTCTGG 60.808 63.158 0.00 0.00 0.00 3.86
3824 4211 2.155194 CGCGAGCGAAAGTCCTCTG 61.155 63.158 12.58 0.00 42.83 3.35
3825 4212 2.179517 CGCGAGCGAAAGTCCTCT 59.820 61.111 12.58 0.00 42.83 3.69
4154 4541 1.003573 GGATCTGGACAGGGACCCT 59.996 63.158 7.44 7.44 0.00 4.34


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

AutoCloner maintained by Alex Coulton.