Multiple sequence alignment - TraesCS4A01G393200

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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 TraesCS4A01G393200 chr4A 100.000 3302 0 0 1 3302 668851848 668855149 0.000000e+00 6098.0
1 TraesCS4A01G393200 chr4A 94.899 1392 43 2 865 2254 669466739 669468104 0.000000e+00 2152.0
2 TraesCS4A01G393200 chr4A 88.320 1387 129 11 951 2334 707177791 707179147 0.000000e+00 1633.0
3 TraesCS4A01G393200 chr4A 88.320 1387 129 11 951 2334 707201316 707202672 0.000000e+00 1633.0
4 TraesCS4A01G393200 chr4A 90.388 1238 111 5 959 2192 707478301 707477068 0.000000e+00 1620.0
5 TraesCS4A01G393200 chr4A 87.808 1378 138 15 951 2325 707402865 707404215 0.000000e+00 1587.0
6 TraesCS4A01G393200 chr4A 87.268 1398 146 14 941 2334 705889383 705890752 0.000000e+00 1567.0
7 TraesCS4A01G393200 chr4A 92.271 828 62 2 2477 3302 669000492 669001319 0.000000e+00 1173.0
8 TraesCS4A01G393200 chr4A 91.898 827 65 2 2477 3301 668709755 668710581 0.000000e+00 1155.0
9 TraesCS4A01G393200 chr4A 86.425 442 50 9 2442 2880 17669961 17670395 2.980000e-130 475.0
10 TraesCS4A01G393200 chr4A 90.556 180 13 3 2247 2422 669482959 669483138 5.510000e-58 235.0
11 TraesCS4A01G393200 chr4A 96.296 108 4 0 865 972 668792222 668792115 9.420000e-41 178.0
12 TraesCS4A01G393200 chr4A 90.678 118 11 0 69 186 668702708 668702825 1.230000e-34 158.0
13 TraesCS4A01G393200 chr4A 88.793 116 13 0 71 186 668792864 668792749 3.430000e-30 143.0
14 TraesCS4A01G393200 chr4A 97.222 36 1 0 36 71 719554705 719554740 9.890000e-06 62.1
15 TraesCS4A01G393200 chr7A 91.806 2453 145 28 3 2422 57220215 57217786 0.000000e+00 3365.0
16 TraesCS4A01G393200 chr7A 87.387 444 51 5 2441 2880 12801959 12802401 3.800000e-139 505.0
17 TraesCS4A01G393200 chr7A 88.208 424 48 2 2879 3302 12803283 12803704 3.800000e-139 505.0
18 TraesCS4A01G393200 chr7A 80.077 261 47 4 2632 2889 306349770 306350028 4.350000e-44 189.0
19 TraesCS4A01G393200 chr7D 96.850 1492 47 0 865 2356 53793363 53791872 0.000000e+00 2495.0
20 TraesCS4A01G393200 chr7D 88.442 1393 125 15 951 2334 24032601 24033966 0.000000e+00 1648.0
21 TraesCS4A01G393200 chr7D 89.794 1264 109 11 900 2147 24157267 24156008 0.000000e+00 1602.0
22 TraesCS4A01G393200 chr7D 89.167 120 11 1 69 186 53793600 53793481 7.380000e-32 148.0
23 TraesCS4A01G393200 chr7D 90.588 85 8 0 2338 2422 53791819 53791735 2.690000e-21 113.0
24 TraesCS4A01G393200 chr7D 87.912 91 11 0 69 159 53962638 53962728 1.250000e-19 108.0
25 TraesCS4A01G393200 chr7D 90.141 71 7 0 2352 2422 53788670 53788600 3.510000e-15 93.5
26 TraesCS4A01G393200 chr7D 93.617 47 2 1 29 75 21267724 21267769 5.910000e-08 69.4
27 TraesCS4A01G393200 chrUn 89.491 1199 120 3 951 2146 220054959 220056154 0.000000e+00 1511.0
28 TraesCS4A01G393200 chr6B 89.671 426 39 5 2879 3302 234663640 234663218 3.750000e-149 538.0
29 TraesCS4A01G393200 chr6B 87.529 425 51 2 2879 3302 439059355 439059778 1.060000e-134 490.0
30 TraesCS4A01G393200 chr2D 88.915 424 47 0 2879 3302 557881473 557881896 1.050000e-144 523.0
31 TraesCS4A01G393200 chr4B 88.889 423 42 5 2884 3302 561392468 561392047 1.760000e-142 516.0
32 TraesCS4A01G393200 chr4B 88.208 424 49 1 2879 3302 182230310 182230732 3.800000e-139 505.0
33 TraesCS4A01G393200 chr4B 87.162 444 52 5 2441 2880 460159442 460159000 1.770000e-137 499.0
34 TraesCS4A01G393200 chr1D 87.822 427 48 4 2879 3302 138268943 138269368 6.360000e-137 497.0
35 TraesCS4A01G393200 chr1D 84.910 444 59 7 2441 2880 63605092 63604653 3.020000e-120 442.0
36 TraesCS4A01G393200 chr5D 86.712 444 55 4 2441 2880 550662387 550662830 1.060000e-134 490.0
37 TraesCS4A01G393200 chr2B 86.486 444 48 11 2442 2880 393108145 393108581 8.290000e-131 477.0
38 TraesCS4A01G393200 chr5A 85.973 442 50 10 2445 2880 565483184 565482749 2.320000e-126 462.0
39 TraesCS4A01G393200 chr1A 100.000 33 0 0 37 69 158712501 158712533 9.890000e-06 62.1
40 TraesCS4A01G393200 chr1A 97.143 35 1 0 36 70 467406573 467406539 3.560000e-05 60.2
41 TraesCS4A01G393200 chr3D 97.143 35 1 0 36 70 578187619 578187585 3.560000e-05 60.2
42 TraesCS4A01G393200 chr3A 100.000 32 0 0 36 67 675230562 675230593 3.560000e-05 60.2
43 TraesCS4A01G393200 chr2A 89.362 47 4 1 27 72 10501792 10501838 1.280000e-04 58.4
44 TraesCS4A01G393200 chr7B 94.444 36 1 1 36 71 56094524 56094558 2.000000e-03 54.7


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 TraesCS4A01G393200 chr4A 668851848 668855149 3301 False 6098.000 6098 100.0000 1 3302 1 chr4A.!!$F4 3301
1 TraesCS4A01G393200 chr4A 669466739 669468104 1365 False 2152.000 2152 94.8990 865 2254 1 chr4A.!!$F6 1389
2 TraesCS4A01G393200 chr4A 707177791 707179147 1356 False 1633.000 1633 88.3200 951 2334 1 chr4A.!!$F9 1383
3 TraesCS4A01G393200 chr4A 707201316 707202672 1356 False 1633.000 1633 88.3200 951 2334 1 chr4A.!!$F10 1383
4 TraesCS4A01G393200 chr4A 707477068 707478301 1233 True 1620.000 1620 90.3880 959 2192 1 chr4A.!!$R1 1233
5 TraesCS4A01G393200 chr4A 707402865 707404215 1350 False 1587.000 1587 87.8080 951 2325 1 chr4A.!!$F11 1374
6 TraesCS4A01G393200 chr4A 705889383 705890752 1369 False 1567.000 1567 87.2680 941 2334 1 chr4A.!!$F8 1393
7 TraesCS4A01G393200 chr4A 669000492 669001319 827 False 1173.000 1173 92.2710 2477 3302 1 chr4A.!!$F5 825
8 TraesCS4A01G393200 chr4A 668709755 668710581 826 False 1155.000 1155 91.8980 2477 3301 1 chr4A.!!$F3 824
9 TraesCS4A01G393200 chr7A 57217786 57220215 2429 True 3365.000 3365 91.8060 3 2422 1 chr7A.!!$R1 2419
10 TraesCS4A01G393200 chr7A 12801959 12803704 1745 False 505.000 505 87.7975 2441 3302 2 chr7A.!!$F2 861
11 TraesCS4A01G393200 chr7D 24032601 24033966 1365 False 1648.000 1648 88.4420 951 2334 1 chr7D.!!$F2 1383
12 TraesCS4A01G393200 chr7D 24156008 24157267 1259 True 1602.000 1602 89.7940 900 2147 1 chr7D.!!$R1 1247
13 TraesCS4A01G393200 chr7D 53788600 53793600 5000 True 712.375 2495 91.6865 69 2422 4 chr7D.!!$R2 2353
14 TraesCS4A01G393200 chrUn 220054959 220056154 1195 False 1511.000 1511 89.4910 951 2146 1 chrUn.!!$F1 1195

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
663 676 0.101759 TCGGATAGCTGCAACGGTAC 59.898 55.0 1.02 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2429 2576 0.102481 GGAGCGCTAACGATGGAAGA 59.898 55.0 11.5 0.0 43.93 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
99 100 1.680338 GGCAGGTGGTCATCCATAAC 58.320 55.000 0.00 0.00 46.20 1.89
106 107 1.281577 TGGTCATCCATAACAGCTGCA 59.718 47.619 15.27 1.58 39.03 4.41
126 127 2.287977 ACAAAGGGGTAGTTGCTTCC 57.712 50.000 0.00 0.00 0.00 3.46
183 186 1.141645 TGAACGCATGGTCGTACAAC 58.858 50.000 0.00 0.00 42.46 3.32
184 187 0.441145 GAACGCATGGTCGTACAACC 59.559 55.000 0.00 0.00 42.46 3.77
191 194 2.465860 TGGTCGTACAACCATCCTTG 57.534 50.000 0.14 0.00 44.40 3.61
192 195 1.972075 TGGTCGTACAACCATCCTTGA 59.028 47.619 0.14 0.00 44.40 3.02
193 196 2.369203 TGGTCGTACAACCATCCTTGAA 59.631 45.455 0.14 0.00 44.40 2.69
194 197 3.000727 GGTCGTACAACCATCCTTGAAG 58.999 50.000 0.00 0.00 39.27 3.02
204 207 6.180472 CAACCATCCTTGAAGTACATTACCT 58.820 40.000 0.00 0.00 0.00 3.08
213 216 8.478877 CCTTGAAGTACATTACCTACTCAAGAT 58.521 37.037 9.45 0.00 34.89 2.40
220 223 5.877012 ACATTACCTACTCAAGATGCAACTG 59.123 40.000 0.00 0.00 0.00 3.16
268 273 7.395190 AACATACAAAGAGATAAATGCTGCA 57.605 32.000 4.13 4.13 0.00 4.41
277 282 5.244626 AGAGATAAATGCTGCAAAGGTTTGT 59.755 36.000 6.36 0.53 40.24 2.83
287 292 2.580589 CAAAGGTTTGTATCGGCAACG 58.419 47.619 0.00 0.00 47.00 4.10
307 312 1.006086 CGTTTGCTCGTGCCATATCA 58.994 50.000 7.05 0.00 38.71 2.15
325 330 6.487668 CCATATCATCCATGCACTTACAGAAA 59.512 38.462 0.00 0.00 0.00 2.52
387 392 8.100508 TCGTGTTAAATCATTGTATCAAACCA 57.899 30.769 0.00 0.00 0.00 3.67
391 396 8.233868 TGTTAAATCATTGTATCAAACCAGTCG 58.766 33.333 0.00 0.00 0.00 4.18
399 404 6.721571 TGTATCAAACCAGTCGAGATTTTC 57.278 37.500 0.00 0.00 0.00 2.29
408 413 9.667107 AAACCAGTCGAGATTTTCTAATTATGA 57.333 29.630 0.00 0.00 0.00 2.15
423 428 9.653516 TTCTAATTATGAAGGCCCAATTTATCA 57.346 29.630 0.00 0.00 0.00 2.15
469 476 4.854399 CAGTTATGCACGAACTTTCCAAA 58.146 39.130 12.11 0.00 34.90 3.28
480 487 8.424731 GCACGAACTTTCCAAAACTATTAATTG 58.575 33.333 0.00 0.00 0.00 2.32
491 498 9.139174 CCAAAACTATTAATTGTCGCTCAAAAT 57.861 29.630 2.97 0.00 39.62 1.82
507 515 8.660373 TCGCTCAAAATAAAACAACAAAACAAT 58.340 25.926 0.00 0.00 0.00 2.71
549 557 6.347061 AATGAGAAATAGAAATGGTCCCCT 57.653 37.500 0.00 0.00 0.00 4.79
557 565 1.215423 GAAATGGTCCCCTGGTGCTAT 59.785 52.381 0.00 0.00 0.00 2.97
583 591 3.207265 ACCCAAATCAAACCCTTTTGC 57.793 42.857 0.00 0.00 41.78 3.68
586 594 3.549794 CCAAATCAAACCCTTTTGCCAA 58.450 40.909 0.00 0.00 41.78 4.52
609 622 2.093306 GTGGTCATCCAACATCGACA 57.907 50.000 0.00 0.00 46.15 4.35
663 676 0.101759 TCGGATAGCTGCAACGGTAC 59.898 55.000 1.02 0.00 0.00 3.34
665 678 1.538204 CGGATAGCTGCAACGGTACAT 60.538 52.381 1.02 0.00 0.00 2.29
668 681 0.899019 TAGCTGCAACGGTACATCCA 59.101 50.000 1.02 0.00 35.57 3.41
732 752 1.396648 CGCGTCAATAATTGGCAGACA 59.603 47.619 0.00 0.00 34.15 3.41
745 765 1.388547 GCAGACAACAACCACTTGGA 58.611 50.000 1.14 0.00 38.94 3.53
760 780 4.543692 CACTTGGACTCTTTCAAAGCATG 58.456 43.478 0.00 0.00 38.73 4.06
765 785 6.707440 TGGACTCTTTCAAAGCATGTTTAA 57.293 33.333 0.00 0.00 0.00 1.52
766 786 6.738114 TGGACTCTTTCAAAGCATGTTTAAG 58.262 36.000 0.00 0.00 0.00 1.85
767 787 6.321181 TGGACTCTTTCAAAGCATGTTTAAGT 59.679 34.615 0.00 0.00 0.00 2.24
768 788 7.500892 TGGACTCTTTCAAAGCATGTTTAAGTA 59.499 33.333 0.00 0.00 0.00 2.24
769 789 8.515414 GGACTCTTTCAAAGCATGTTTAAGTAT 58.485 33.333 0.00 0.00 0.00 2.12
770 790 9.899226 GACTCTTTCAAAGCATGTTTAAGTATT 57.101 29.630 0.00 0.00 0.00 1.89
831 851 7.461749 TGGAGACATATTTCTGAGGAAAACTT 58.538 34.615 0.00 0.00 39.15 2.66
841 861 8.438676 TTTCTGAGGAAAACTTTTCTACTCTG 57.561 34.615 12.88 13.89 38.35 3.35
842 862 7.125792 TCTGAGGAAAACTTTTCTACTCTGT 57.874 36.000 12.88 0.00 0.00 3.41
859 879 1.678627 CTGTGTAGTCTGATCGGAGGG 59.321 57.143 3.91 0.00 0.00 4.30
875 913 3.732470 GGAATGCCGTCGATTCCC 58.268 61.111 12.55 0.00 42.16 3.97
897 935 6.383147 TCCCTCCGAATCTCATTAGTAAAGTT 59.617 38.462 0.00 0.00 0.00 2.66
910 948 6.476243 TTAGTAAAGTTCCGATGAAGCAAC 57.524 37.500 0.00 0.00 0.00 4.17
1195 1239 3.228017 TCGTCGACAAGGCCACCA 61.228 61.111 17.16 0.00 0.00 4.17
1392 1436 2.117156 GGAGTACCGTCTAGCGCCA 61.117 63.158 2.29 0.00 39.71 5.69
1650 1696 3.130160 CTGCCTTTGGAGCTCGCC 61.130 66.667 7.83 0.00 0.00 5.54
1770 1828 4.144727 ATCGACCCTCCGGCCTCT 62.145 66.667 0.00 0.00 0.00 3.69
1793 1851 2.261430 ATCTCATCGCTGGCTTGCCA 62.261 55.000 14.10 14.10 0.00 4.92
1794 1852 2.437180 TCATCGCTGGCTTGCCAG 60.437 61.111 30.97 30.97 40.47 4.85
1953 2011 1.079127 CGAGGAGCACGGTTTCCAT 60.079 57.895 10.20 0.00 35.88 3.41
2013 2071 0.179097 GGAGCCTCGTGGAGTTCATC 60.179 60.000 7.92 0.00 34.57 2.92
2053 2117 0.886490 GCCTGCGAATCCTATGGTGG 60.886 60.000 0.00 0.00 0.00 4.61
2054 2118 0.469917 CCTGCGAATCCTATGGTGGT 59.530 55.000 0.00 0.00 0.00 4.16
2055 2119 1.586422 CTGCGAATCCTATGGTGGTG 58.414 55.000 0.00 0.00 0.00 4.17
2283 2359 1.539496 GCAGTTCCGTGGAGTTGTGTA 60.539 52.381 0.00 0.00 0.00 2.90
2291 2367 3.186409 CCGTGGAGTTGTGTAATCAACAG 59.814 47.826 11.22 0.00 46.78 3.16
2345 2492 6.018343 ACGCAAAAATAAATGGGAAACACTTG 60.018 34.615 0.00 0.00 34.03 3.16
2355 2502 7.833285 AATGGGAAACACTTGTATACAGTTT 57.167 32.000 17.07 17.07 35.33 2.66
2413 2560 0.817013 TGATGCTTTTCCAATCCCGC 59.183 50.000 0.00 0.00 0.00 6.13
2416 2563 2.340328 GCTTTTCCAATCCCGCGGT 61.340 57.895 26.12 2.55 0.00 5.68
2422 2569 1.254026 TCCAATCCCGCGGTCTATAG 58.746 55.000 26.12 7.54 0.00 1.31
2423 2570 0.389948 CCAATCCCGCGGTCTATAGC 60.390 60.000 26.12 0.00 0.00 2.97
2435 2582 5.117355 CGGTCTATAGCGTTTATCTTCCA 57.883 43.478 0.00 0.00 41.60 3.53
2436 2583 5.710984 CGGTCTATAGCGTTTATCTTCCAT 58.289 41.667 0.00 0.00 41.60 3.41
2438 2585 5.800941 GGTCTATAGCGTTTATCTTCCATCG 59.199 44.000 0.00 0.00 0.00 3.84
2439 2586 6.380190 GTCTATAGCGTTTATCTTCCATCGT 58.620 40.000 0.00 0.00 0.00 3.73
2444 2591 3.361724 GCGTTTATCTTCCATCGTTAGCG 60.362 47.826 0.00 0.00 39.92 4.26
2455 2602 3.198489 GTTAGCGCTCCAGCAGGC 61.198 66.667 16.34 0.00 42.21 4.85
2470 2617 1.466697 GCAGGCGCGCTAAATTTACAA 60.467 47.619 32.29 0.00 0.00 2.41
2475 2622 2.511879 CGCGCTAAATTTACAACCCAC 58.488 47.619 5.56 0.00 0.00 4.61
2480 2627 4.142773 CGCTAAATTTACAACCCACACGAT 60.143 41.667 0.00 0.00 0.00 3.73
2537 2685 7.728895 ACAAAGAAGATCAAACAAACAAAACG 58.271 30.769 0.00 0.00 0.00 3.60
2546 2694 9.618410 GATCAAACAAACAAAACGTAAATCAAG 57.382 29.630 0.00 0.00 0.00 3.02
2755 4104 2.363018 CCTCGCAGTCCTCCTCCA 60.363 66.667 0.00 0.00 0.00 3.86
2772 4121 1.284715 CACACTCGCACAGGACGTA 59.715 57.895 0.00 0.00 0.00 3.57
2786 4135 4.222145 ACAGGACGTACCAACAACTCATAT 59.778 41.667 0.00 0.00 42.04 1.78
2852 4201 6.887626 ATGTTATGCATGATCACATAAGCA 57.112 33.333 15.46 15.44 38.93 3.91
2896 5128 0.247185 TGACCGATAACCGAACCACC 59.753 55.000 0.00 0.00 41.76 4.61
2925 5208 4.334203 TCGGCTTTTTATTGACGTGCATAT 59.666 37.500 0.00 0.00 35.95 1.78
3009 5382 8.501580 CGTAGGACGAACTCATCTACAATATTA 58.498 37.037 0.00 0.00 46.05 0.98
3142 5515 2.203552 TGCAAATGGCCGTTGGGA 60.204 55.556 11.94 6.57 43.89 4.37
3172 5762 0.595310 GGAGGAATAGTGCGCTCGAC 60.595 60.000 9.73 0.00 0.00 4.20
3202 5792 1.410932 CGAGGAGAGAAGGTGGAGGAT 60.411 57.143 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.474630 TGCATGGGCTAGAAAATTTCAAAAT 58.525 32.000 8.55 0.00 41.91 1.82
26 27 3.448301 CCTGCATGGGCTAGAAAATTTCA 59.552 43.478 8.55 0.00 41.91 2.69
27 28 3.448660 ACCTGCATGGGCTAGAAAATTTC 59.551 43.478 0.00 0.00 41.91 2.17
31 32 1.838112 CACCTGCATGGGCTAGAAAA 58.162 50.000 0.00 0.00 41.91 2.29
53 54 1.134788 GGTCCACTAGTCATCAACCCG 60.135 57.143 0.00 0.00 0.00 5.28
99 100 0.883833 CTACCCCTTTGTTGCAGCTG 59.116 55.000 10.11 10.11 0.00 4.24
106 107 2.594131 GGAAGCAACTACCCCTTTGTT 58.406 47.619 0.00 0.00 0.00 2.83
126 127 3.325870 TGAAATAATGCCTATCGCGAGG 58.674 45.455 16.66 12.93 42.08 4.63
159 162 0.037326 ACGACCATGCGTTCATCTGT 60.037 50.000 0.00 0.00 42.71 3.41
183 186 7.125792 AGTAGGTAATGTACTTCAAGGATGG 57.874 40.000 0.00 0.00 0.00 3.51
184 187 7.782049 TGAGTAGGTAATGTACTTCAAGGATG 58.218 38.462 0.00 0.00 30.60 3.51
185 188 7.973048 TGAGTAGGTAATGTACTTCAAGGAT 57.027 36.000 0.00 0.00 30.60 3.24
187 190 7.837863 TCTTGAGTAGGTAATGTACTTCAAGG 58.162 38.462 10.04 0.00 36.92 3.61
188 191 9.307121 CATCTTGAGTAGGTAATGTACTTCAAG 57.693 37.037 4.91 4.91 37.21 3.02
189 192 7.764443 GCATCTTGAGTAGGTAATGTACTTCAA 59.236 37.037 0.00 0.00 30.60 2.69
190 193 7.093509 TGCATCTTGAGTAGGTAATGTACTTCA 60.094 37.037 0.00 0.00 30.60 3.02
191 194 7.265673 TGCATCTTGAGTAGGTAATGTACTTC 58.734 38.462 0.00 0.00 30.60 3.01
192 195 7.182817 TGCATCTTGAGTAGGTAATGTACTT 57.817 36.000 0.00 0.00 30.60 2.24
193 196 6.791867 TGCATCTTGAGTAGGTAATGTACT 57.208 37.500 0.00 0.00 33.25 2.73
194 197 7.010552 CAGTTGCATCTTGAGTAGGTAATGTAC 59.989 40.741 0.00 0.00 0.00 2.90
204 207 8.621532 AATTAAAGACAGTTGCATCTTGAGTA 57.378 30.769 1.16 0.00 35.34 2.59
247 252 7.123247 ACCTTTGCAGCATTTATCTCTTTGTAT 59.877 33.333 0.00 0.00 0.00 2.29
248 253 6.434028 ACCTTTGCAGCATTTATCTCTTTGTA 59.566 34.615 0.00 0.00 0.00 2.41
257 262 6.035843 CGATACAAACCTTTGCAGCATTTAT 58.964 36.000 0.00 0.00 41.79 1.40
258 263 5.398169 CGATACAAACCTTTGCAGCATTTA 58.602 37.500 0.00 0.00 41.79 1.40
268 273 1.068816 GCGTTGCCGATACAAACCTTT 60.069 47.619 0.00 0.00 35.63 3.11
287 292 0.316196 GATATGGCACGAGCAAACGC 60.316 55.000 7.26 0.00 44.61 4.84
289 294 2.031682 GGATGATATGGCACGAGCAAAC 60.032 50.000 7.26 0.00 44.61 2.93
307 312 6.350445 GGAATGTTTTCTGTAAGTGCATGGAT 60.350 38.462 0.00 0.00 33.76 3.41
325 330 1.956477 AGCAGCTTTTCGTGGAATGTT 59.044 42.857 0.00 0.00 0.00 2.71
364 369 9.341899 GACTGGTTTGATACAATGATTTAACAC 57.658 33.333 0.00 0.00 0.00 3.32
384 389 9.319143 CTTCATAATTAGAAAATCTCGACTGGT 57.681 33.333 0.00 0.00 0.00 4.00
387 392 7.442666 GGCCTTCATAATTAGAAAATCTCGACT 59.557 37.037 0.00 0.00 0.00 4.18
391 396 7.823745 TGGGCCTTCATAATTAGAAAATCTC 57.176 36.000 4.53 0.00 0.00 2.75
399 404 9.696917 GTTGATAAATTGGGCCTTCATAATTAG 57.303 33.333 4.53 0.00 0.00 1.73
408 413 3.056891 CACGTGTTGATAAATTGGGCCTT 60.057 43.478 7.58 0.00 0.00 4.35
458 463 8.635983 GCGACAATTAATAGTTTTGGAAAGTTC 58.364 33.333 0.00 0.00 0.00 3.01
459 464 8.357402 AGCGACAATTAATAGTTTTGGAAAGTT 58.643 29.630 0.00 0.00 0.00 2.66
462 469 7.877003 TGAGCGACAATTAATAGTTTTGGAAA 58.123 30.769 0.00 0.00 0.00 3.13
464 471 7.441890 TTGAGCGACAATTAATAGTTTTGGA 57.558 32.000 0.00 0.00 33.18 3.53
480 487 7.449027 TGTTTTGTTGTTTTATTTTGAGCGAC 58.551 30.769 0.00 0.00 0.00 5.19
545 553 1.680338 GTTAGCAATAGCACCAGGGG 58.320 55.000 0.00 0.00 45.49 4.79
546 554 1.680338 GGTTAGCAATAGCACCAGGG 58.320 55.000 0.00 0.00 45.49 4.45
547 555 1.064758 TGGGTTAGCAATAGCACCAGG 60.065 52.381 0.00 0.00 45.49 4.45
549 557 2.889170 TTGGGTTAGCAATAGCACCA 57.111 45.000 0.00 0.00 45.49 4.17
557 565 3.582164 AGGGTTTGATTTGGGTTAGCAA 58.418 40.909 0.00 0.00 0.00 3.91
586 594 1.339055 CGATGTTGGATGACCACCTGT 60.339 52.381 0.00 0.00 46.80 4.00
597 605 5.124776 GGACCATATTTTTGTCGATGTTGGA 59.875 40.000 0.00 0.00 0.00 3.53
647 660 2.135933 GGATGTACCGTTGCAGCTATC 58.864 52.381 0.00 0.00 0.00 2.08
689 702 5.177142 CGTGCATGGTCAAATTTCATTTTCA 59.823 36.000 0.00 0.00 0.00 2.69
698 711 0.109781 GACGCGTGCATGGTCAAATT 60.110 50.000 20.70 0.00 0.00 1.82
709 722 0.179176 TGCCAATTATTGACGCGTGC 60.179 50.000 20.70 11.45 0.00 5.34
710 723 1.396648 TCTGCCAATTATTGACGCGTG 59.603 47.619 20.70 0.00 0.00 5.34
732 752 3.963129 TGAAAGAGTCCAAGTGGTTGTT 58.037 40.909 0.00 0.00 36.34 2.83
801 821 7.199167 TCCTCAGAAATATGTCTCCATGAAA 57.801 36.000 0.00 0.00 32.29 2.69
841 861 2.054232 TCCCTCCGATCAGACTACAC 57.946 55.000 0.00 0.00 0.00 2.90
842 862 2.820728 TTCCCTCCGATCAGACTACA 57.179 50.000 0.00 0.00 0.00 2.74
859 879 0.880718 GGAGGGAATCGACGGCATTC 60.881 60.000 0.00 5.23 0.00 2.67
875 913 6.418226 CGGAACTTTACTAATGAGATTCGGAG 59.582 42.308 0.00 0.00 0.00 4.63
897 935 4.185413 GCGAGTTGCTTCATCGGA 57.815 55.556 0.00 0.00 41.73 4.55
910 948 6.030548 TCTCATGGGATTTTATAGAGCGAG 57.969 41.667 0.00 0.00 0.00 5.03
1016 1060 2.290260 TGGTTGTGATTCGCTGGAGAAT 60.290 45.455 0.00 0.00 42.92 2.40
1392 1436 2.370445 CGCAGGGATGGGGAACTCT 61.370 63.158 0.00 0.00 0.00 3.24
1650 1696 2.027625 GGCTTCGTTGTCGTCCCAG 61.028 63.158 0.00 0.00 38.33 4.45
1770 1828 1.117994 AAGCCAGCGATGAGATCTCA 58.882 50.000 27.03 27.03 44.59 3.27
1953 2011 0.394488 CCCTCAGCGGACTGTAGAGA 60.394 60.000 0.00 0.00 44.77 3.10
2013 2071 2.674380 GAGGTGGGCTGCTGGTTG 60.674 66.667 0.00 0.00 0.00 3.77
2218 2294 0.391130 GCGTTACCAGCAGTCATCCA 60.391 55.000 0.00 0.00 34.19 3.41
2283 2359 6.705302 TGTCATCTAGAAGAAGCTGTTGATT 58.295 36.000 0.00 0.00 0.00 2.57
2291 2367 2.468831 CGGCTGTCATCTAGAAGAAGC 58.531 52.381 16.85 16.85 0.00 3.86
2317 2393 7.711339 AGTGTTTCCCATTTATTTTTGCGTTAA 59.289 29.630 0.00 0.00 0.00 2.01
2374 2521 2.013807 CGGCACATGACCCGTATTG 58.986 57.895 16.85 0.00 39.67 1.90
2375 2522 4.532490 CGGCACATGACCCGTATT 57.468 55.556 16.85 0.00 39.67 1.89
2413 2560 5.117355 TGGAAGATAAACGCTATAGACCG 57.883 43.478 3.21 0.75 0.00 4.79
2416 2563 6.570672 ACGATGGAAGATAAACGCTATAGA 57.429 37.500 3.21 0.00 0.00 1.98
2422 2569 3.361724 CGCTAACGATGGAAGATAAACGC 60.362 47.826 0.00 0.00 43.93 4.84
2423 2570 3.361724 GCGCTAACGATGGAAGATAAACG 60.362 47.826 0.00 0.00 43.93 3.60
2424 2571 3.802685 AGCGCTAACGATGGAAGATAAAC 59.197 43.478 8.99 0.00 43.93 2.01
2425 2572 4.049186 GAGCGCTAACGATGGAAGATAAA 58.951 43.478 11.50 0.00 43.93 1.40
2427 2574 2.030185 GGAGCGCTAACGATGGAAGATA 60.030 50.000 11.50 0.00 43.93 1.98
2429 2576 0.102481 GGAGCGCTAACGATGGAAGA 59.898 55.000 11.50 0.00 43.93 2.87
2431 2578 0.179111 CTGGAGCGCTAACGATGGAA 60.179 55.000 11.50 0.00 43.93 3.53
2432 2579 1.437573 CTGGAGCGCTAACGATGGA 59.562 57.895 11.50 0.00 43.93 3.41
2433 2580 2.240500 GCTGGAGCGCTAACGATGG 61.241 63.158 11.50 0.00 43.93 3.51
2435 2582 1.227089 CTGCTGGAGCGCTAACGAT 60.227 57.895 11.50 0.00 45.83 3.73
2436 2583 2.181777 CTGCTGGAGCGCTAACGA 59.818 61.111 11.50 0.00 45.83 3.85
2438 2585 3.198489 GCCTGCTGGAGCGCTAAC 61.198 66.667 11.50 7.38 45.83 2.34
2439 2586 4.819761 CGCCTGCTGGAGCGCTAA 62.820 66.667 11.50 0.00 46.50 3.09
2455 2602 2.095668 TGTGGGTTGTAAATTTAGCGCG 60.096 45.455 0.00 0.00 0.00 6.86
2470 2617 0.179032 TTTGTGCTGATCGTGTGGGT 60.179 50.000 0.00 0.00 0.00 4.51
2475 2622 2.753989 TGTTGTTTGTGCTGATCGTG 57.246 45.000 0.00 0.00 0.00 4.35
2480 2627 6.094742 TGAGTAAGAAATGTTGTTTGTGCTGA 59.905 34.615 0.00 0.00 0.00 4.26
2755 4104 1.285023 GTACGTCCTGTGCGAGTGT 59.715 57.895 0.00 0.00 0.00 3.55
2772 4121 6.299141 ACTGTTCTCAATATGAGTTGTTGGT 58.701 36.000 7.21 0.00 44.58 3.67
2786 4135 5.596361 TGGCCAAAATTTAGACTGTTCTCAA 59.404 36.000 0.61 0.00 32.75 3.02
2896 5128 2.908626 GTCAATAAAAAGCCGAAGCACG 59.091 45.455 0.00 0.00 43.56 5.34
2925 5208 4.219115 GAGGACCTCACAATGATCCTAGA 58.781 47.826 17.10 0.00 36.35 2.43
2972 5255 2.569059 TCGTCCTACGATTCTTCCGAT 58.431 47.619 0.00 0.00 46.73 4.18
3022 5395 9.469807 TTGGTGCATGTTGTTTATAGTTTTAAG 57.530 29.630 0.00 0.00 0.00 1.85
3032 5405 6.757237 AGATGAATTTGGTGCATGTTGTTTA 58.243 32.000 0.00 0.00 0.00 2.01
3142 5515 4.702131 GCACTATTCCTCCAATGAACAACT 59.298 41.667 0.00 0.00 0.00 3.16
3177 5767 3.144193 CCTTCTCTCCTCGCCGCT 61.144 66.667 0.00 0.00 0.00 5.52
3218 5808 3.068881 CTTCCACCGCTTCTCCCA 58.931 61.111 0.00 0.00 0.00 4.37
3223 5813 3.479269 CGACGCTTCCACCGCTTC 61.479 66.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.