Multiple sequence alignment - TraesCS3B01G361700

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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 TraesCS3B01G361700 chr3B 100.000 2540 0 0 1 2540 573402732 573405271 0.000000e+00 4691.0
1 TraesCS3B01G361700 chr3B 82.143 168 26 4 91 255 637786650 637786816 9.470000e-30 141.0
2 TraesCS3B01G361700 chr3D 88.122 985 45 35 1319 2235 437967662 437968642 0.000000e+00 1105.0
3 TraesCS3B01G361700 chr3D 82.993 735 88 12 36 742 397533377 397532652 4.610000e-177 630.0
4 TraesCS3B01G361700 chr3D 97.143 280 6 1 975 1254 437966538 437966815 2.960000e-129 472.0
5 TraesCS3B01G361700 chr3D 94.481 308 13 3 2235 2540 437968688 437968993 2.960000e-129 472.0
6 TraesCS3B01G361700 chr3D 94.631 149 8 0 779 927 437966037 437966185 5.460000e-57 231.0
7 TraesCS3B01G361700 chr3D 75.749 367 69 17 7 363 486122528 486122884 1.560000e-37 167.0
8 TraesCS3B01G361700 chr3D 95.745 47 2 0 743 789 437961663 437961709 2.710000e-10 76.8
9 TraesCS3B01G361700 chr3A 94.872 468 22 2 744 1210 576208698 576209164 0.000000e+00 730.0
10 TraesCS3B01G361700 chr3A 90.877 559 24 12 1311 1856 576210269 576210813 0.000000e+00 725.0
11 TraesCS3B01G361700 chr3A 83.642 324 37 6 36 344 673468740 673468418 8.890000e-75 291.0
12 TraesCS3B01G361700 chr3A 85.560 277 14 10 2253 2526 576212592 576212845 1.500000e-67 267.0
13 TraesCS3B01G361700 chr3A 80.098 407 28 26 1860 2235 576212106 576212490 1.170000e-63 254.0
14 TraesCS3B01G361700 chr3A 79.883 343 47 13 404 742 673468203 673467879 5.460000e-57 231.0
15 TraesCS3B01G361700 chr6B 83.651 734 90 13 36 742 163957306 163958036 0.000000e+00 664.0
16 TraesCS3B01G361700 chr6B 78.629 248 46 5 96 339 103155553 103155309 9.410000e-35 158.0
17 TraesCS3B01G361700 chr6D 82.967 728 98 13 36 744 327370075 327370795 3.560000e-178 634.0
18 TraesCS3B01G361700 chr1D 83.407 675 84 11 93 742 469091089 469091760 3.620000e-168 601.0
19 TraesCS3B01G361700 chr2B 81.768 724 90 21 36 741 789534054 789533355 3.670000e-158 568.0
20 TraesCS3B01G361700 chr4A 81.928 664 97 14 73 716 703809713 703810373 7.990000e-150 540.0
21 TraesCS3B01G361700 chr5B 83.252 615 74 13 148 742 652802764 652802159 2.880000e-149 538.0
22 TraesCS3B01G361700 chr5B 84.390 205 25 5 545 743 652804336 652804539 7.170000e-46 195.0
23 TraesCS3B01G361700 chr5A 83.569 353 44 6 404 742 442544007 442543655 4.080000e-83 318.0
24 TraesCS3B01G361700 chr5A 80.176 227 26 10 1044 1269 657757051 657757259 4.380000e-33 152.0
25 TraesCS3B01G361700 chr5A 77.820 266 38 13 997 1247 657725193 657725452 7.320000e-31 145.0
26 TraesCS3B01G361700 chr5A 80.628 191 25 5 1042 1223 657760372 657760559 1.230000e-28 137.0
27 TraesCS3B01G361700 chr2A 77.833 406 64 14 1 402 526313456 526313839 7.070000e-56 228.0
28 TraesCS3B01G361700 chr5D 83.071 254 34 3 995 1242 529845178 529845428 3.290000e-54 222.0
29 TraesCS3B01G361700 chr5D 80.000 215 29 7 1042 1255 529815860 529816061 2.040000e-31 147.0
30 TraesCS3B01G361700 chr5D 76.207 290 40 20 996 1271 529800917 529801191 2.650000e-25 126.0
31 TraesCS3B01G361700 chr5D 91.667 48 2 1 291 336 472314946 472314899 5.870000e-07 65.8
32 TraesCS3B01G361700 chr7D 81.455 275 44 5 1 274 11137863 11137595 4.250000e-53 219.0
33 TraesCS3B01G361700 chr7D 80.608 263 38 9 75 335 607563141 607563392 9.270000e-45 191.0
34 TraesCS3B01G361700 chr7D 100.000 29 0 0 291 319 597090313 597090341 1.000000e-03 54.7
35 TraesCS3B01G361700 chr1B 78.869 336 54 12 1 322 564737550 564737218 7.120000e-51 211.0
36 TraesCS3B01G361700 chr4B 77.593 241 42 7 1 236 32184588 32184355 4.410000e-28 135.0


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 TraesCS3B01G361700 chr3B 573402732 573405271 2539 False 4691 4691 100.00000 1 2540 1 chr3B.!!$F1 2539
1 TraesCS3B01G361700 chr3D 397532652 397533377 725 True 630 630 82.99300 36 742 1 chr3D.!!$R1 706
2 TraesCS3B01G361700 chr3D 437966037 437968993 2956 False 570 1105 93.59425 779 2540 4 chr3D.!!$F3 1761
3 TraesCS3B01G361700 chr3A 576208698 576212845 4147 False 494 730 87.85175 744 2526 4 chr3A.!!$F1 1782
4 TraesCS3B01G361700 chr3A 673467879 673468740 861 True 261 291 81.76250 36 742 2 chr3A.!!$R1 706
5 TraesCS3B01G361700 chr6B 163957306 163958036 730 False 664 664 83.65100 36 742 1 chr6B.!!$F1 706
6 TraesCS3B01G361700 chr6D 327370075 327370795 720 False 634 634 82.96700 36 744 1 chr6D.!!$F1 708
7 TraesCS3B01G361700 chr1D 469091089 469091760 671 False 601 601 83.40700 93 742 1 chr1D.!!$F1 649
8 TraesCS3B01G361700 chr2B 789533355 789534054 699 True 568 568 81.76800 36 741 1 chr2B.!!$R1 705
9 TraesCS3B01G361700 chr4A 703809713 703810373 660 False 540 540 81.92800 73 716 1 chr4A.!!$F1 643
10 TraesCS3B01G361700 chr5B 652802159 652802764 605 True 538 538 83.25200 148 742 1 chr5B.!!$R1 594

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
647 837 0.098728 ATGCAACCGAAACGCTATGC 59.901 50.0 0.0 0.0 0.0 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 5196 0.550914 TTCCAGTGCAGAAACCACCT 59.449 50.0 0.0 0.0 33.75 4.0 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
28 29 4.680237 CAGTCAGCCGCCGGACAA 62.680 66.667 7.68 0.00 38.44 3.18
29 30 4.379243 AGTCAGCCGCCGGACAAG 62.379 66.667 7.68 0.00 38.44 3.16
89 99 3.676605 ACGACGACGATGGCACCA 61.677 61.111 15.32 0.00 42.66 4.17
127 137 3.670377 GGGCAGGGCAAACACGAC 61.670 66.667 0.00 0.00 0.00 4.34
157 167 3.070446 TGGTCGTGCCATATAGGGTTTAG 59.930 47.826 5.15 0.00 43.61 1.85
158 168 3.070590 GGTCGTGCCATATAGGGTTTAGT 59.929 47.826 5.15 0.00 38.09 2.24
266 282 1.463528 CGAATTTCGCGAGGTTGGTTC 60.464 52.381 9.59 7.84 31.14 3.62
278 294 1.067821 GGTTGGTTCGAATTGTTGGCA 59.932 47.619 0.00 0.00 0.00 4.92
279 295 2.288763 GGTTGGTTCGAATTGTTGGCAT 60.289 45.455 0.00 0.00 0.00 4.40
289 305 0.808125 TTGTTGGCATGATGTACGCC 59.192 50.000 0.00 2.07 46.43 5.68
336 355 4.570663 CGTCCGCGGACTGATCCC 62.571 72.222 44.83 24.97 42.83 3.85
344 363 1.760875 GGACTGATCCCCGTGCCTA 60.761 63.158 0.00 0.00 39.39 3.93
345 364 1.335132 GGACTGATCCCCGTGCCTAA 61.335 60.000 0.00 0.00 39.39 2.69
346 365 0.179081 GACTGATCCCCGTGCCTAAC 60.179 60.000 0.00 0.00 0.00 2.34
349 368 4.171103 ATCCCCGTGCCTAACCGC 62.171 66.667 0.00 0.00 0.00 5.68
355 374 4.832608 GTGCCTAACCGCGGAGGG 62.833 72.222 35.90 28.22 46.96 4.30
365 384 2.203209 GCGGAGGGATGCGGATTT 60.203 61.111 0.00 0.00 0.00 2.17
366 385 1.823899 GCGGAGGGATGCGGATTTT 60.824 57.895 0.00 0.00 0.00 1.82
367 386 1.384222 GCGGAGGGATGCGGATTTTT 61.384 55.000 0.00 0.00 0.00 1.94
394 413 1.455408 GCAGTTTGCCGTTAAACATGC 59.545 47.619 12.43 13.40 41.76 4.06
403 422 3.086282 CCGTTAAACATGCCCTTAGGTT 58.914 45.455 0.00 0.00 34.57 3.50
404 423 4.263435 CCGTTAAACATGCCCTTAGGTTA 58.737 43.478 0.00 0.00 34.57 2.85
406 425 5.220970 CCGTTAAACATGCCCTTAGGTTATG 60.221 44.000 9.49 9.49 36.49 1.90
422 599 4.719273 AGGTTATGAGAGAGAAGGGAAAGG 59.281 45.833 0.00 0.00 0.00 3.11
430 607 1.073923 GAGAAGGGAAAGGAAGCACCA 59.926 52.381 2.96 0.00 42.04 4.17
569 753 1.273327 GGTGTTTCCTCTTTGCCATGG 59.727 52.381 7.63 7.63 0.00 3.66
636 826 3.499737 GCGTCTCCCATGCAACCG 61.500 66.667 0.00 0.00 36.94 4.44
638 828 1.375396 CGTCTCCCATGCAACCGAA 60.375 57.895 0.00 0.00 0.00 4.30
643 833 2.625823 CCCATGCAACCGAAACGCT 61.626 57.895 0.00 0.00 0.00 5.07
647 837 0.098728 ATGCAACCGAAACGCTATGC 59.901 50.000 0.00 0.00 0.00 3.14
678 873 4.025229 CGTGACAAGGTCAGATTCGAAAAA 60.025 41.667 0.00 0.00 43.57 1.94
703 899 4.196193 TCAGAAACAAGGTCAATTCGTGT 58.804 39.130 0.00 0.00 0.00 4.49
716 912 5.038033 TCAATTCGTGTTTAAGTTTGCCAC 58.962 37.500 0.00 0.00 0.00 5.01
731 927 0.954452 GCCACAAAGGTCAGAACAGG 59.046 55.000 0.00 0.00 40.61 4.00
742 938 3.058224 GGTCAGAACAGGAATTTTGTCCG 60.058 47.826 0.00 0.00 43.03 4.79
745 941 2.107552 AGAACAGGAATTTTGTCCGGGA 59.892 45.455 0.00 0.00 43.03 5.14
746 942 2.200373 ACAGGAATTTTGTCCGGGAG 57.800 50.000 0.00 0.00 43.03 4.30
843 1039 0.251073 GGGATTCGGGAAAAGTCGGA 59.749 55.000 0.00 0.00 0.00 4.55
844 1040 1.653151 GGATTCGGGAAAAGTCGGAG 58.347 55.000 0.00 0.00 0.00 4.63
942 1138 2.624316 TAATACATCGCCGACGGATC 57.376 50.000 20.50 0.00 40.63 3.36
961 1157 1.843832 GTATCCTCCTCCCCCTGCC 60.844 68.421 0.00 0.00 0.00 4.85
1038 1539 2.416260 GTCGTAGGATCGGTGGCC 59.584 66.667 0.00 0.00 0.00 5.36
1085 1586 1.012486 GTGCCGTTTACTCAGACCCG 61.012 60.000 0.00 0.00 0.00 5.28
1249 1750 2.836360 CCGTAAGCCCCCTCGCTA 60.836 66.667 0.00 0.00 38.44 4.26
1250 1751 2.416260 CGTAAGCCCCCTCGCTAC 59.584 66.667 0.00 0.00 38.44 3.58
1251 1752 2.820261 GTAAGCCCCCTCGCTACC 59.180 66.667 0.00 0.00 38.44 3.18
1252 1753 2.445274 TAAGCCCCCTCGCTACCC 60.445 66.667 0.00 0.00 38.44 3.69
1276 1777 2.846665 CCCCCTCTCTCTCTTTCTCT 57.153 55.000 0.00 0.00 0.00 3.10
1277 1778 2.666317 CCCCCTCTCTCTCTTTCTCTC 58.334 57.143 0.00 0.00 0.00 3.20
1278 1779 2.244769 CCCCCTCTCTCTCTTTCTCTCT 59.755 54.545 0.00 0.00 0.00 3.10
1279 1780 3.290710 CCCCTCTCTCTCTTTCTCTCTG 58.709 54.545 0.00 0.00 0.00 3.35
1280 1781 3.309121 CCCCTCTCTCTCTTTCTCTCTGT 60.309 52.174 0.00 0.00 0.00 3.41
1281 1782 3.947834 CCCTCTCTCTCTTTCTCTCTGTC 59.052 52.174 0.00 0.00 0.00 3.51
1286 1787 5.647658 TCTCTCTCTTTCTCTCTGTCATGTC 59.352 44.000 0.00 0.00 0.00 3.06
1293 1794 2.023598 TCTCTCTGTCATGTCCATCCCT 60.024 50.000 0.00 0.00 0.00 4.20
1294 1795 2.102757 CTCTCTGTCATGTCCATCCCTG 59.897 54.545 0.00 0.00 0.00 4.45
1297 1798 1.280133 CTGTCATGTCCATCCCTGTGT 59.720 52.381 0.00 0.00 0.00 3.72
1306 1807 0.392193 CATCCCTGTGTGAGTGAGGC 60.392 60.000 0.00 0.00 0.00 4.70
1322 2947 2.225091 TGAGGCCCAACTCATGATGTTT 60.225 45.455 0.00 0.00 42.26 2.83
1425 3050 3.916061 TGAATAATTTCAGGCGCGC 57.084 47.368 25.94 25.94 36.94 6.86
1463 3088 1.065102 CTGCAGCTATGGTGTTGATGC 59.935 52.381 0.00 0.00 43.65 3.91
1471 3096 2.785540 TGGTGTTGATGCAGCTATCA 57.214 45.000 2.53 0.00 37.70 2.15
1544 3169 4.416620 TCTTGCAAGTTGTTTTAACCACG 58.583 39.130 25.19 0.00 30.56 4.94
1565 3196 7.064728 ACCACGTCTCTAAATAAAATTCTCTGC 59.935 37.037 0.00 0.00 0.00 4.26
1567 3198 8.113062 CACGTCTCTAAATAAAATTCTCTGCAG 58.887 37.037 7.63 7.63 0.00 4.41
1584 3215 9.982651 TTCTCTGCAGTATTATTGTACTATTCC 57.017 33.333 14.67 0.00 33.29 3.01
1585 3216 8.297426 TCTCTGCAGTATTATTGTACTATTCCG 58.703 37.037 14.67 0.00 33.29 4.30
1586 3217 7.948357 TCTGCAGTATTATTGTACTATTCCGT 58.052 34.615 14.67 0.00 33.29 4.69
1608 3264 5.276348 CGTTTTGCCTTTTGATTGACTTGTC 60.276 40.000 0.00 0.00 0.00 3.18
1677 3338 9.745880 TTATATCTGACCGTTAGAATTTCAGAC 57.254 33.333 6.01 0.00 44.09 3.51
1691 3352 8.336801 AGAATTTCAGACGGTTTAGCTTAAAT 57.663 30.769 0.00 0.00 0.00 1.40
1692 3353 8.237267 AGAATTTCAGACGGTTTAGCTTAAATG 58.763 33.333 0.00 0.00 0.00 2.32
1693 3354 4.939509 TCAGACGGTTTAGCTTAAATGC 57.060 40.909 0.00 0.00 0.00 3.56
1695 3356 4.941263 TCAGACGGTTTAGCTTAAATGCAT 59.059 37.500 0.00 0.00 34.99 3.96
1696 3357 6.110033 TCAGACGGTTTAGCTTAAATGCATA 58.890 36.000 0.00 0.00 34.99 3.14
1699 3364 7.915397 CAGACGGTTTAGCTTAAATGCATATTT 59.085 33.333 0.00 0.00 39.69 1.40
1727 3392 4.159135 AGTTGATTTAGCTTTGCCTGATGG 59.841 41.667 0.00 0.00 0.00 3.51
1731 3396 3.940209 TTAGCTTTGCCTGATGGTTTG 57.060 42.857 0.00 0.00 35.27 2.93
1735 3400 2.819608 GCTTTGCCTGATGGTTTGTCTA 59.180 45.455 0.00 0.00 35.27 2.59
1736 3401 3.119708 GCTTTGCCTGATGGTTTGTCTAG 60.120 47.826 0.00 0.00 35.27 2.43
1737 3402 3.788227 TTGCCTGATGGTTTGTCTAGT 57.212 42.857 0.00 0.00 35.27 2.57
1738 3403 4.901197 TTGCCTGATGGTTTGTCTAGTA 57.099 40.909 0.00 0.00 35.27 1.82
1739 3404 4.202245 TGCCTGATGGTTTGTCTAGTAC 57.798 45.455 0.00 0.00 35.27 2.73
1750 3415 5.356470 GGTTTGTCTAGTACGTATGAGAGGT 59.644 44.000 0.00 0.00 0.00 3.85
1791 3456 3.882326 CTGCGGCCAGGGATCCAT 61.882 66.667 15.23 2.55 35.38 3.41
1858 4819 8.046708 TGTTTGATAACTGCATTAGTGTAGGAT 58.953 33.333 8.15 1.29 41.74 3.24
1876 4838 9.372369 GTGTAGGATAGAGGAATGCAAATATAC 57.628 37.037 0.00 0.00 0.00 1.47
1940 4925 5.132502 ACCTGCATTTTGATATTCGATCCA 58.867 37.500 0.00 0.00 0.00 3.41
1947 4932 8.453320 GCATTTTGATATTCGATCCATCATACA 58.547 33.333 5.31 0.00 0.00 2.29
1951 4936 9.723601 TTTGATATTCGATCCATCATACATTCA 57.276 29.630 5.31 0.00 0.00 2.57
1952 4937 9.895138 TTGATATTCGATCCATCATACATTCAT 57.105 29.630 5.31 0.00 0.00 2.57
1955 4940 9.770097 ATATTCGATCCATCATACATTCATACC 57.230 33.333 0.00 0.00 0.00 2.73
1985 4979 5.140454 TCACTGCCTATTAGCTGACATAGA 58.860 41.667 0.00 0.00 35.80 1.98
2140 5139 9.065871 CCACGCAAAGAAATAAGAATAAAAGAG 57.934 33.333 0.00 0.00 0.00 2.85
2193 5196 5.576447 AAAAAGAAAGGCGTGAGAAAGAA 57.424 34.783 0.00 0.00 0.00 2.52
2235 5238 2.478134 CGCCTTGAGTCTCTGTTTTCTG 59.522 50.000 0.65 0.00 0.00 3.02
2236 5239 3.733337 GCCTTGAGTCTCTGTTTTCTGA 58.267 45.455 0.65 0.00 0.00 3.27
2387 5490 5.969423 AGTGTGAATTAAATCAATGGCCAG 58.031 37.500 13.05 0.00 0.00 4.85
2390 5493 4.807304 GTGAATTAAATCAATGGCCAGCAG 59.193 41.667 13.05 3.19 0.00 4.24
2476 5582 6.571150 GCAGTTGAAGGTCTTGCTTAATCAAT 60.571 38.462 0.00 0.00 0.00 2.57
2484 5590 8.593945 AGGTCTTGCTTAATCAATAATTTCCA 57.406 30.769 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.680237 TTGTCCGGCGGCTGACTG 62.680 66.667 28.56 4.53 32.67 3.51
12 13 4.379243 CTTGTCCGGCGGCTGACT 62.379 66.667 28.56 0.00 32.67 3.41
65 66 2.674033 ATCGTCGTCGTGGTCCCA 60.674 61.111 1.33 0.00 38.33 4.37
107 117 2.521708 GTGTTTGCCCTGCCCTGT 60.522 61.111 0.00 0.00 0.00 4.00
114 124 0.038526 CTCGTAGTCGTGTTTGCCCT 60.039 55.000 0.00 0.00 38.33 5.19
115 125 1.012486 CCTCGTAGTCGTGTTTGCCC 61.012 60.000 0.00 0.00 38.33 5.36
119 129 1.000938 GACCACCTCGTAGTCGTGTTT 60.001 52.381 0.00 0.00 38.33 2.83
120 130 0.595095 GACCACCTCGTAGTCGTGTT 59.405 55.000 0.00 0.00 38.33 3.32
121 131 1.572085 CGACCACCTCGTAGTCGTGT 61.572 60.000 4.87 0.00 46.23 4.49
254 270 0.872388 ACAATTCGAACCAACCTCGC 59.128 50.000 0.00 0.00 36.25 5.03
255 271 2.350388 CCAACAATTCGAACCAACCTCG 60.350 50.000 0.00 0.00 37.66 4.63
266 282 3.353524 CGTACATCATGCCAACAATTCG 58.646 45.455 0.00 0.00 0.00 3.34
278 294 1.113517 ACCCTAGCGGCGTACATCAT 61.114 55.000 9.37 0.00 33.26 2.45
279 295 1.324740 AACCCTAGCGGCGTACATCA 61.325 55.000 9.37 0.00 33.26 3.07
289 305 0.527817 GACGACATCCAACCCTAGCG 60.528 60.000 0.00 0.00 0.00 4.26
349 368 2.793831 AAAAATCCGCATCCCTCCG 58.206 52.632 0.00 0.00 0.00 4.63
376 395 1.000394 GGGCATGTTTAACGGCAAACT 60.000 47.619 12.27 0.30 38.85 2.66
378 397 1.333177 AGGGCATGTTTAACGGCAAA 58.667 45.000 12.27 0.00 0.00 3.68
381 400 1.404035 CCTAAGGGCATGTTTAACGGC 59.596 52.381 0.00 3.47 0.00 5.68
383 402 5.587043 TCATAACCTAAGGGCATGTTTAACG 59.413 40.000 0.00 0.00 35.63 3.18
394 413 4.591072 CCCTTCTCTCTCATAACCTAAGGG 59.409 50.000 0.00 0.00 44.29 3.95
403 422 4.407296 GCTTCCTTTCCCTTCTCTCTCATA 59.593 45.833 0.00 0.00 0.00 2.15
404 423 3.199727 GCTTCCTTTCCCTTCTCTCTCAT 59.800 47.826 0.00 0.00 0.00 2.90
406 425 2.569404 TGCTTCCTTTCCCTTCTCTCTC 59.431 50.000 0.00 0.00 0.00 3.20
422 599 2.050985 GTGCAACGCTGGTGCTTC 60.051 61.111 17.16 8.61 36.97 3.86
430 607 0.611200 TACCCTGTATGTGCAACGCT 59.389 50.000 0.00 0.00 42.39 5.07
470 649 3.545633 GTTGTTCATCTGTTTCTCGTGC 58.454 45.455 0.00 0.00 0.00 5.34
474 653 4.540824 GCTTGGTTGTTCATCTGTTTCTC 58.459 43.478 0.00 0.00 0.00 2.87
477 656 2.948979 TCGCTTGGTTGTTCATCTGTTT 59.051 40.909 0.00 0.00 0.00 2.83
514 693 5.712917 TGGTCACCATCTATATATGTGCGTA 59.287 40.000 0.00 0.00 0.00 4.42
516 695 5.072040 TGGTCACCATCTATATATGTGCG 57.928 43.478 0.00 0.00 0.00 5.34
520 699 5.351465 GGCGTTTGGTCACCATCTATATATG 59.649 44.000 0.00 0.00 31.53 1.78
521 700 5.012664 TGGCGTTTGGTCACCATCTATATAT 59.987 40.000 0.00 0.00 31.53 0.86
522 701 4.345547 TGGCGTTTGGTCACCATCTATATA 59.654 41.667 0.00 0.00 31.53 0.86
523 702 3.135712 TGGCGTTTGGTCACCATCTATAT 59.864 43.478 0.00 0.00 31.53 0.86
551 735 0.968405 GCCATGGCAAAGAGGAAACA 59.032 50.000 32.08 0.00 41.49 2.83
576 760 2.030562 CCCACACTCGTCCGCTTT 59.969 61.111 0.00 0.00 0.00 3.51
579 763 3.916392 CTGACCCACACTCGTCCGC 62.916 68.421 0.00 0.00 0.00 5.54
609 793 4.139234 GGAGACGCCACGGTACCC 62.139 72.222 6.25 0.00 36.34 3.69
612 796 2.363276 ATGGGAGACGCCACGGTA 60.363 61.111 0.00 0.00 38.95 4.02
636 826 1.548986 GCCAACATGCATAGCGTTTC 58.451 50.000 0.00 0.00 0.00 2.78
638 828 1.429021 CGCCAACATGCATAGCGTT 59.571 52.632 18.81 9.14 41.78 4.84
643 833 1.468127 CTTGTCACGCCAACATGCATA 59.532 47.619 0.00 0.00 0.00 3.14
647 837 0.238289 GACCTTGTCACGCCAACATG 59.762 55.000 0.00 0.00 32.09 3.21
678 873 6.183360 ACACGAATTGACCTTGTTTCTGAATT 60.183 34.615 0.00 0.00 0.00 2.17
703 899 4.707448 TCTGACCTTTGTGGCAAACTTAAA 59.293 37.500 0.00 0.00 40.22 1.52
716 912 5.906073 ACAAAATTCCTGTTCTGACCTTTG 58.094 37.500 0.00 0.00 0.00 2.77
731 927 1.280998 TCCTCCTCCCGGACAAAATTC 59.719 52.381 0.73 0.00 34.92 2.17
742 938 1.135960 CTGGATTCCTTCCTCCTCCC 58.864 60.000 3.95 0.00 45.68 4.30
745 941 0.253347 TGGCTGGATTCCTTCCTCCT 60.253 55.000 3.95 0.00 45.68 3.69
746 942 0.849417 ATGGCTGGATTCCTTCCTCC 59.151 55.000 3.95 0.00 45.68 4.30
747 943 1.478288 CCATGGCTGGATTCCTTCCTC 60.478 57.143 0.00 0.00 46.37 3.71
812 1008 1.895020 CGAATCCCGAGGGGTTGACA 61.895 60.000 12.08 0.00 44.74 3.58
843 1039 4.371417 TCCTACCACGTCCCCGCT 62.371 66.667 0.00 0.00 37.70 5.52
844 1040 4.139234 GTCCTACCACGTCCCCGC 62.139 72.222 0.00 0.00 37.70 6.13
860 1056 1.893801 GATGGAATAGGATCGTCGGGT 59.106 52.381 0.00 0.00 0.00 5.28
942 1138 2.210711 GCAGGGGGAGGAGGATACG 61.211 68.421 0.00 0.00 46.39 3.06
1038 1539 1.520342 GAGTAGCAAGAGCAGGGCG 60.520 63.158 0.00 0.00 45.49 6.13
1167 1668 1.507174 GTCGAGGTCGTTCTCCTGG 59.493 63.158 0.00 0.00 40.80 4.45
1170 1671 1.134281 GACGTCGAGGTCGTTCTCC 59.866 63.158 21.13 0.00 41.64 3.71
1242 1743 2.523657 GGGGTAGGGGTAGCGAGG 60.524 72.222 0.00 0.00 0.00 4.63
1268 1769 4.161189 GGATGGACATGACAGAGAGAAAGA 59.839 45.833 0.00 0.00 0.00 2.52
1269 1770 4.440880 GGATGGACATGACAGAGAGAAAG 58.559 47.826 0.00 0.00 0.00 2.62
1270 1771 3.198635 GGGATGGACATGACAGAGAGAAA 59.801 47.826 0.00 0.00 0.00 2.52
1271 1772 2.768527 GGGATGGACATGACAGAGAGAA 59.231 50.000 0.00 0.00 0.00 2.87
1272 1773 2.023598 AGGGATGGACATGACAGAGAGA 60.024 50.000 0.00 0.00 0.00 3.10
1273 1774 2.102757 CAGGGATGGACATGACAGAGAG 59.897 54.545 0.00 0.00 0.00 3.20
1274 1775 2.113807 CAGGGATGGACATGACAGAGA 58.886 52.381 0.00 0.00 0.00 3.10
1275 1776 1.836166 ACAGGGATGGACATGACAGAG 59.164 52.381 0.00 0.00 0.00 3.35
1276 1777 1.556451 CACAGGGATGGACATGACAGA 59.444 52.381 0.00 0.00 0.00 3.41
1277 1778 1.280133 ACACAGGGATGGACATGACAG 59.720 52.381 0.00 0.00 0.00 3.51
1278 1779 1.003464 CACACAGGGATGGACATGACA 59.997 52.381 0.00 0.00 0.00 3.58
1279 1780 1.278985 TCACACAGGGATGGACATGAC 59.721 52.381 0.00 0.00 0.00 3.06
1280 1781 1.556451 CTCACACAGGGATGGACATGA 59.444 52.381 0.00 0.00 0.00 3.07
1281 1782 1.280133 ACTCACACAGGGATGGACATG 59.720 52.381 0.00 0.00 0.00 3.21
1286 1787 0.251354 CCTCACTCACACAGGGATGG 59.749 60.000 0.00 0.00 32.40 3.51
1293 1794 1.148273 GTTGGGCCTCACTCACACA 59.852 57.895 4.53 0.00 0.00 3.72
1294 1795 0.603975 GAGTTGGGCCTCACTCACAC 60.604 60.000 23.76 7.23 0.00 3.82
1297 1798 0.325933 CATGAGTTGGGCCTCACTCA 59.674 55.000 29.64 29.64 43.86 3.41
1306 1807 4.949238 TCATGGTAAACATCATGAGTTGGG 59.051 41.667 0.09 0.00 43.09 4.12
1408 3033 0.317854 GGGCGCGCCTGAAATTATTC 60.318 55.000 45.23 23.69 36.10 1.75
1425 3050 0.324091 AGATCCTTGCAAAGCTGGGG 60.324 55.000 0.00 0.00 44.44 4.96
1463 3088 3.117491 ACCATGTCCGATTGATAGCTG 57.883 47.619 0.00 0.00 0.00 4.24
1471 3096 2.006888 CACGCTAAACCATGTCCGATT 58.993 47.619 0.00 0.00 0.00 3.34
1563 3194 8.951787 AAACGGAATAGTACAATAATACTGCA 57.048 30.769 0.00 0.00 36.09 4.41
1565 3196 9.646336 GCAAAACGGAATAGTACAATAATACTG 57.354 33.333 0.00 0.00 36.09 2.74
1567 3198 8.833493 AGGCAAAACGGAATAGTACAATAATAC 58.167 33.333 0.00 0.00 0.00 1.89
1572 3203 6.584185 AAAGGCAAAACGGAATAGTACAAT 57.416 33.333 0.00 0.00 0.00 2.71
1574 3205 5.531659 TCAAAAGGCAAAACGGAATAGTACA 59.468 36.000 0.00 0.00 0.00 2.90
1575 3206 6.004408 TCAAAAGGCAAAACGGAATAGTAC 57.996 37.500 0.00 0.00 0.00 2.73
1577 3208 5.722021 ATCAAAAGGCAAAACGGAATAGT 57.278 34.783 0.00 0.00 0.00 2.12
1578 3209 6.089417 GTCAATCAAAAGGCAAAACGGAATAG 59.911 38.462 0.00 0.00 0.00 1.73
1579 3210 5.923684 GTCAATCAAAAGGCAAAACGGAATA 59.076 36.000 0.00 0.00 0.00 1.75
1580 3211 4.749598 GTCAATCAAAAGGCAAAACGGAAT 59.250 37.500 0.00 0.00 0.00 3.01
1583 3214 3.716601 AGTCAATCAAAAGGCAAAACGG 58.283 40.909 0.00 0.00 0.00 4.44
1584 3215 4.566360 ACAAGTCAATCAAAAGGCAAAACG 59.434 37.500 0.00 0.00 0.00 3.60
1585 3216 5.812127 AGACAAGTCAATCAAAAGGCAAAAC 59.188 36.000 2.72 0.00 0.00 2.43
1586 3217 5.976458 AGACAAGTCAATCAAAAGGCAAAA 58.024 33.333 2.72 0.00 0.00 2.44
1608 3264 2.301346 CTAATTGCTGCCCAGGGTAAG 58.699 52.381 7.55 6.66 0.00 2.34
1631 3287 2.666272 TGGGCAGGTTAATGTGAACA 57.334 45.000 0.00 0.00 0.00 3.18
1632 3288 5.852282 ATAATGGGCAGGTTAATGTGAAC 57.148 39.130 0.00 0.00 0.00 3.18
1633 3289 7.448161 CAGATATAATGGGCAGGTTAATGTGAA 59.552 37.037 0.00 0.00 0.00 3.18
1695 3356 7.706179 GGCAAAGCTAAATCAACTGCATAAATA 59.294 33.333 0.00 0.00 0.00 1.40
1696 3357 6.536224 GGCAAAGCTAAATCAACTGCATAAAT 59.464 34.615 0.00 0.00 0.00 1.40
1699 3364 4.706476 AGGCAAAGCTAAATCAACTGCATA 59.294 37.500 0.00 0.00 0.00 3.14
1727 3392 6.434018 ACCTCTCATACGTACTAGACAAAC 57.566 41.667 0.00 0.00 0.00 2.93
1731 3396 6.534793 GGCTATACCTCTCATACGTACTAGAC 59.465 46.154 0.00 0.00 34.51 2.59
1735 3400 4.252073 CGGCTATACCTCTCATACGTACT 58.748 47.826 0.00 0.00 35.61 2.73
1736 3401 3.181512 GCGGCTATACCTCTCATACGTAC 60.182 52.174 0.00 0.00 35.61 3.67
1737 3402 3.005554 GCGGCTATACCTCTCATACGTA 58.994 50.000 0.00 0.00 35.61 3.57
1738 3403 1.811359 GCGGCTATACCTCTCATACGT 59.189 52.381 0.00 0.00 35.61 3.57
1739 3404 1.810755 TGCGGCTATACCTCTCATACG 59.189 52.381 0.00 0.00 35.61 3.06
1750 3415 2.798145 CGAACATCACAGTGCGGCTATA 60.798 50.000 0.00 0.00 36.90 1.31
1791 3456 2.385013 TTCTGCTCGCTGCTATTTCA 57.615 45.000 0.00 0.00 43.37 2.69
1876 4838 8.816640 AAGGTTGCATTTTTCTACATACAAAG 57.183 30.769 0.00 0.00 0.00 2.77
1887 4849 9.815936 CATCAAGAAATAAAGGTTGCATTTTTC 57.184 29.630 0.00 0.00 0.00 2.29
1940 4925 8.435187 AGTGATGACAAGGTATGAATGTATGAT 58.565 33.333 0.00 0.00 0.00 2.45
1947 4932 4.080129 AGGCAGTGATGACAAGGTATGAAT 60.080 41.667 0.00 0.00 0.00 2.57
1948 4933 3.264193 AGGCAGTGATGACAAGGTATGAA 59.736 43.478 0.00 0.00 0.00 2.57
1949 4934 2.840038 AGGCAGTGATGACAAGGTATGA 59.160 45.455 0.00 0.00 0.00 2.15
1950 4935 3.272574 AGGCAGTGATGACAAGGTATG 57.727 47.619 0.00 0.00 0.00 2.39
1951 4936 5.636903 AATAGGCAGTGATGACAAGGTAT 57.363 39.130 0.00 0.00 0.00 2.73
1952 4937 5.453339 GCTAATAGGCAGTGATGACAAGGTA 60.453 44.000 0.00 0.00 0.00 3.08
1953 4938 4.684485 GCTAATAGGCAGTGATGACAAGGT 60.684 45.833 0.00 0.00 0.00 3.50
1954 4939 3.812053 GCTAATAGGCAGTGATGACAAGG 59.188 47.826 0.00 0.00 0.00 3.61
1955 4940 4.510711 CAGCTAATAGGCAGTGATGACAAG 59.489 45.833 0.00 0.00 34.17 3.16
1985 4979 3.442996 GCACATGGCGTCTAGAAGT 57.557 52.632 7.53 0.00 0.00 3.01
2193 5196 0.550914 TTCCAGTGCAGAAACCACCT 59.449 50.000 0.00 0.00 33.75 4.00
2317 5410 9.914834 TGGTATTGGATAGCTGTACTTATTTTT 57.085 29.630 0.00 0.00 34.47 1.94
2318 5411 9.561069 CTGGTATTGGATAGCTGTACTTATTTT 57.439 33.333 0.00 0.00 34.47 1.82
2319 5412 8.714906 ACTGGTATTGGATAGCTGTACTTATTT 58.285 33.333 0.00 0.00 41.51 1.40
2320 5413 8.263854 ACTGGTATTGGATAGCTGTACTTATT 57.736 34.615 0.00 0.00 41.51 1.40
2321 5414 7.857404 ACTGGTATTGGATAGCTGTACTTAT 57.143 36.000 0.00 0.00 41.51 1.73
2322 5415 7.563924 AGAACTGGTATTGGATAGCTGTACTTA 59.436 37.037 0.00 0.00 42.14 2.24
2387 5490 1.671979 TTGGCACTCATCTATGCTGC 58.328 50.000 0.00 0.00 41.74 5.25
2390 5493 2.854963 TGGATTGGCACTCATCTATGC 58.145 47.619 7.18 0.00 41.29 3.14
2484 5590 9.594936 AAAGTGTAGCTGAATATATAGACTCCT 57.405 33.333 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.