Multiple sequence alignment - TraesCS2B01G419600

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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 TraesCS2B01G419600 chr2B 100.000 3007 0 0 1 3007 601214156 601211150 0.000000e+00 5553.0
1 TraesCS2B01G419600 chr2B 88.145 523 38 8 1 499 760834097 760834619 4.290000e-168 601.0
2 TraesCS2B01G419600 chr2B 87.380 523 42 3 1 499 601268472 601267950 2.010000e-161 579.0
3 TraesCS2B01G419600 chr2A 91.625 2376 120 44 501 2862 655220121 655217811 0.000000e+00 3212.0
4 TraesCS2B01G419600 chr2A 80.196 510 61 22 1 499 764651638 764652118 2.220000e-91 346.0
5 TraesCS2B01G419600 chr2D 93.523 1621 53 20 565 2157 512043697 512042101 0.000000e+00 2364.0
6 TraesCS2B01G419600 chr2D 87.520 625 72 6 2370 2991 512041245 512040624 0.000000e+00 717.0
7 TraesCS2B01G419600 chr2D 82.486 531 58 18 1 499 624182002 624182529 1.660000e-117 433.0
8 TraesCS2B01G419600 chr2D 88.660 194 13 6 2155 2340 512041809 512041617 8.390000e-56 228.0
9 TraesCS2B01G419600 chr2D 78.333 360 69 8 2588 2942 469462350 469461995 1.080000e-54 224.0
10 TraesCS2B01G419600 chr7B 87.954 523 39 7 1 499 48241242 48241764 2.000000e-166 595.0
11 TraesCS2B01G419600 chr7B 86.857 525 40 11 1 499 669324892 669324371 7.280000e-156 560.0
12 TraesCS2B01G419600 chr1B 87.791 516 43 7 1 499 463815751 463816263 1.200000e-163 586.0
13 TraesCS2B01G419600 chr6B 87.380 523 42 7 1 499 122789725 122790247 2.010000e-161 579.0
14 TraesCS2B01G419600 chr6B 86.807 523 44 10 1 499 216445352 216445873 7.280000e-156 560.0
15 TraesCS2B01G419600 chr6B 95.000 100 5 0 400 499 500214359 500214260 1.120000e-34 158.0
16 TraesCS2B01G419600 chr3B 86.616 523 44 9 1 499 130133374 130133894 3.390000e-154 555.0
17 TraesCS2B01G419600 chr3B 91.294 402 33 2 1 400 130182066 130182467 5.670000e-152 547.0
18 TraesCS2B01G419600 chr3B 93.000 100 7 0 401 500 563405210 563405111 2.420000e-31 147.0
19 TraesCS2B01G419600 chr3B 84.483 116 16 2 2378 2493 548368762 548368649 2.450000e-21 113.0
20 TraesCS2B01G419600 chr3B 87.000 100 10 3 2377 2475 548549254 548549157 3.170000e-20 110.0
21 TraesCS2B01G419600 chr3B 82.906 117 17 3 2377 2493 548835645 548835532 5.300000e-18 102.0
22 TraesCS2B01G419600 chr3B 80.909 110 17 3 2384 2493 279689683 279689788 1.920000e-12 84.2
23 TraesCS2B01G419600 chr7D 82.409 523 59 14 1 499 268557554 268557041 2.770000e-115 425.0
24 TraesCS2B01G419600 chr7D 81.768 181 28 5 2562 2738 596552548 596552369 2.420000e-31 147.0
25 TraesCS2B01G419600 chr4B 80.626 511 57 25 1 499 4554413 4554893 1.030000e-94 357.0
26 TraesCS2B01G419600 chrUn 81.410 468 45 20 56 499 35183239 35183688 7.980000e-91 344.0
27 TraesCS2B01G419600 chrUn 81.410 468 45 20 56 499 35188960 35189409 7.980000e-91 344.0
28 TraesCS2B01G419600 chrUn 81.622 185 27 7 2564 2743 50980036 50979854 2.420000e-31 147.0
29 TraesCS2B01G419600 chrUn 80.909 110 21 0 2384 2493 29719278 29719169 1.480000e-13 87.9
30 TraesCS2B01G419600 chr5D 80.387 362 47 12 162 499 559885813 559886174 1.380000e-63 254.0
31 TraesCS2B01G419600 chr5D 83.246 191 27 5 1029 1215 352219256 352219445 1.430000e-38 171.0
32 TraesCS2B01G419600 chr5D 80.303 198 33 6 1025 1219 353478115 353478309 8.690000e-31 145.0
33 TraesCS2B01G419600 chr5B 83.511 188 26 5 1032 1215 416851121 416850935 1.430000e-38 171.0
34 TraesCS2B01G419600 chr5B 80.808 198 32 6 1025 1219 417438511 417438705 1.870000e-32 150.0
35 TraesCS2B01G419600 chr5B 100.000 28 0 0 2507 2534 529664620 529664647 5.000000e-03 52.8
36 TraesCS2B01G419600 chr5A 82.447 188 28 5 1032 1215 453877101 453876915 3.100000e-35 159.0
37 TraesCS2B01G419600 chr5A 78.846 208 37 7 1025 1228 454397162 454397366 1.880000e-27 134.0
38 TraesCS2B01G419600 chr5A 79.562 137 17 6 2324 2460 241189878 241189753 1.480000e-13 87.9
39 TraesCS2B01G419600 chr5A 79.091 110 23 0 2384 2493 706151684 706151575 3.210000e-10 76.8
40 TraesCS2B01G419600 chr3D 81.522 184 28 6 2560 2738 232920781 232920963 2.420000e-31 147.0
41 TraesCS2B01G419600 chr1D 81.319 182 28 6 2562 2738 149050458 149050278 3.120000e-30 143.0
42 TraesCS2B01G419600 chr1D 80.769 182 29 6 2562 2738 288788329 288788149 1.450000e-28 137.0
43 TraesCS2B01G419600 chr4A 81.765 170 26 5 2562 2727 716524144 716524312 1.450000e-28 137.0
44 TraesCS2B01G419600 chr4A 76.238 202 42 6 1029 1227 19622498 19622300 5.300000e-18 102.0
45 TraesCS2B01G419600 chr6D 75.665 263 52 8 2507 2757 447442087 447441825 1.460000e-23 121.0
46 TraesCS2B01G419600 chr4D 74.619 197 41 9 1032 1225 506340126 506339936 8.940000e-11 78.7


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 TraesCS2B01G419600 chr2B 601211150 601214156 3006 True 5553 5553 100.000 1 3007 1 chr2B.!!$R1 3006
1 TraesCS2B01G419600 chr2B 760834097 760834619 522 False 601 601 88.145 1 499 1 chr2B.!!$F1 498
2 TraesCS2B01G419600 chr2B 601267950 601268472 522 True 579 579 87.380 1 499 1 chr2B.!!$R2 498
3 TraesCS2B01G419600 chr2A 655217811 655220121 2310 True 3212 3212 91.625 501 2862 1 chr2A.!!$R1 2361
4 TraesCS2B01G419600 chr2D 512040624 512043697 3073 True 1103 2364 89.901 565 2991 3 chr2D.!!$R2 2426
5 TraesCS2B01G419600 chr2D 624182002 624182529 527 False 433 433 82.486 1 499 1 chr2D.!!$F1 498
6 TraesCS2B01G419600 chr7B 48241242 48241764 522 False 595 595 87.954 1 499 1 chr7B.!!$F1 498
7 TraesCS2B01G419600 chr7B 669324371 669324892 521 True 560 560 86.857 1 499 1 chr7B.!!$R1 498
8 TraesCS2B01G419600 chr1B 463815751 463816263 512 False 586 586 87.791 1 499 1 chr1B.!!$F1 498
9 TraesCS2B01G419600 chr6B 122789725 122790247 522 False 579 579 87.380 1 499 1 chr6B.!!$F1 498
10 TraesCS2B01G419600 chr6B 216445352 216445873 521 False 560 560 86.807 1 499 1 chr6B.!!$F2 498
11 TraesCS2B01G419600 chr3B 130133374 130133894 520 False 555 555 86.616 1 499 1 chr3B.!!$F1 498
12 TraesCS2B01G419600 chr7D 268557041 268557554 513 True 425 425 82.409 1 499 1 chr7D.!!$R1 498


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
155 168 1.068585 GGACACCGACGACCACTTT 59.931 57.895 0.0 0.0 0.0 2.66 F
1220 1267 0.039437 CTCAACACCTACGTGCGTCT 60.039 55.000 0.0 0.0 44.4 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 1854 0.332972 GTCCTCCTCTGCCCCATTTT 59.667 55.0 0.00 0.0 0.00 1.82 R
2339 2711 0.237235 TTTCTTCCGTTGCATCGCAC 59.763 50.0 11.68 0.0 38.71 5.34 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
93 95 1.345415 TGTACGGGAGAAGGGTGAAAC 59.655 52.381 0.00 0.00 0.00 2.78
127 131 1.923227 CTCTGCGCGACTACTGACCA 61.923 60.000 12.10 0.00 0.00 4.02
135 139 2.786854 CGACTACTGACCAGTTCATCG 58.213 52.381 8.06 10.86 42.54 3.84
155 168 1.068585 GGACACCGACGACCACTTT 59.931 57.895 0.00 0.00 0.00 2.66
204 217 1.873591 ACAACCTCTTCAACGACATGC 59.126 47.619 0.00 0.00 0.00 4.06
209 222 2.093973 CCTCTTCAACGACATGCCTAGT 60.094 50.000 0.00 0.00 0.00 2.57
272 287 5.384063 TGTCCCGTACGTGTTCTTATTTA 57.616 39.130 15.21 0.00 0.00 1.40
354 369 8.597167 AGGCTCTATTTCATATATGCAACTACA 58.403 33.333 7.92 0.00 0.00 2.74
422 459 6.563010 GCATCAGATCGCATGACTTACTTTAC 60.563 42.308 10.26 0.00 0.00 2.01
522 559 8.697292 ACATAGAGTTTTCATACTTACTCCCTC 58.303 37.037 0.00 0.00 38.17 4.30
581 621 8.561212 TCAGTTTTATACACATTTTAGCGTGTT 58.439 29.630 0.00 0.00 43.71 3.32
602 642 7.625309 CGTGTTTGTTCACTCGTTTTAATTTTG 59.375 33.333 0.00 0.00 36.33 2.44
617 658 8.748582 GTTTTAATTTTGTAAAGTGAACGGAGG 58.251 33.333 0.00 0.00 0.00 4.30
629 670 3.635373 GTGAACGGAGGGAGTGTCATATA 59.365 47.826 0.00 0.00 0.00 0.86
684 725 6.981559 GGGTTGCTTAAAACTCAAACAACATA 59.018 34.615 0.00 0.00 38.08 2.29
685 726 7.169140 GGGTTGCTTAAAACTCAAACAACATAG 59.831 37.037 0.00 0.00 38.08 2.23
686 727 7.169140 GGTTGCTTAAAACTCAAACAACATAGG 59.831 37.037 0.00 0.00 38.08 2.57
687 728 7.575414 TGCTTAAAACTCAAACAACATAGGA 57.425 32.000 0.00 0.00 0.00 2.94
688 729 7.648142 TGCTTAAAACTCAAACAACATAGGAG 58.352 34.615 0.00 0.00 0.00 3.69
689 730 7.284489 TGCTTAAAACTCAAACAACATAGGAGT 59.716 33.333 0.00 0.00 40.33 3.85
690 731 8.780249 GCTTAAAACTCAAACAACATAGGAGTA 58.220 33.333 0.00 0.00 37.82 2.59
945 992 3.030291 TGTGCAACCAAACCAAATCTCT 58.970 40.909 0.00 0.00 34.36 3.10
1219 1266 1.615107 GCTCAACACCTACGTGCGTC 61.615 60.000 0.00 0.00 44.40 5.19
1220 1267 0.039437 CTCAACACCTACGTGCGTCT 60.039 55.000 0.00 0.00 44.40 4.18
1222 1269 1.007336 CAACACCTACGTGCGTCTCC 61.007 60.000 0.00 0.00 44.40 3.71
1223 1270 2.202440 CACCTACGTGCGTCTCCG 60.202 66.667 0.00 0.00 32.04 4.63
1240 1287 4.035102 GCTCCACCCACCCACCTC 62.035 72.222 0.00 0.00 0.00 3.85
1241 1288 3.330720 CTCCACCCACCCACCTCC 61.331 72.222 0.00 0.00 0.00 4.30
1246 1293 4.489771 CCCACCCACCTCCGCATC 62.490 72.222 0.00 0.00 0.00 3.91
1247 1294 4.838152 CCACCCACCTCCGCATCG 62.838 72.222 0.00 0.00 0.00 3.84
1250 1297 4.899239 CCCACCTCCGCATCGCTC 62.899 72.222 0.00 0.00 0.00 5.03
1251 1298 4.899239 CCACCTCCGCATCGCTCC 62.899 72.222 0.00 0.00 0.00 4.70
1252 1299 4.899239 CACCTCCGCATCGCTCCC 62.899 72.222 0.00 0.00 0.00 4.30
1302 1352 0.887387 TACCAAGGGTGCTGCGTTTC 60.887 55.000 0.00 0.00 36.19 2.78
1688 1738 2.445085 TATGACCACGGCGGGGAT 60.445 61.111 38.35 21.86 40.22 3.85
1781 1831 3.127352 GAAGAGGTCGCGCGAGGAT 62.127 63.158 35.75 22.04 0.00 3.24
1804 1854 4.172232 CGGGGGAGGGGATGAGGA 62.172 72.222 0.00 0.00 0.00 3.71
1906 1962 3.369471 CGAGAACAAGGGAAGGCTATGAA 60.369 47.826 0.00 0.00 0.00 2.57
2060 2129 5.914085 CGGAAAGCACTAGGATCTAAATG 57.086 43.478 0.00 0.00 0.00 2.32
2064 2133 4.078639 AGCACTAGGATCTAAATGGTGC 57.921 45.455 15.77 15.77 45.73 5.01
2146 2215 3.561725 GGTAGCACAATGTAGAATCAGCC 59.438 47.826 0.00 0.00 0.00 4.85
2150 2219 3.181493 GCACAATGTAGAATCAGCCAAGG 60.181 47.826 0.00 0.00 0.00 3.61
2164 2527 0.872388 CCAAGGCGTGTAGAACAACC 59.128 55.000 0.00 0.00 0.00 3.77
2196 2559 1.353022 TGGTAGTTAGGGCCTGTTTGG 59.647 52.381 18.53 0.00 39.35 3.28
2215 2578 4.069312 TGGTTTCCATGTAGACCTAGGA 57.931 45.455 17.98 0.00 33.33 2.94
2233 2596 6.060788 CCTAGGATTGGGAAAATGAGAAGAG 58.939 44.000 1.05 0.00 0.00 2.85
2264 2634 7.375053 TGCCATGGTTTATTGTAGAGTTTTTC 58.625 34.615 14.67 0.00 0.00 2.29
2285 2655 5.685520 TCTTTTGTAAAAAGGCCAAGGTT 57.314 34.783 5.01 0.00 0.00 3.50
2286 2656 5.423886 TCTTTTGTAAAAAGGCCAAGGTTG 58.576 37.500 5.01 0.00 0.00 3.77
2313 2683 8.823220 ATTTAAGTAGCACAAACCCATAGAAT 57.177 30.769 0.00 0.00 0.00 2.40
2342 2714 8.748380 ATAGAAACTAGCAAAAGAATTTGTGC 57.252 30.769 3.55 0.00 46.19 4.57
2350 2722 4.448005 CAAAAGAATTTGTGCGATGCAAC 58.552 39.130 0.00 0.00 37.62 4.17
2351 2723 1.967762 AGAATTTGTGCGATGCAACG 58.032 45.000 12.54 12.54 41.47 4.10
2420 3139 7.306013 TCATGACTCAAGACCCTAATAGGTAT 58.694 38.462 5.49 0.00 41.42 2.73
2422 3141 9.261035 CATGACTCAAGACCCTAATAGGTATAT 57.739 37.037 5.49 0.00 41.42 0.86
2471 3190 5.104941 CCCATCTGTGTTGTCAGTTATCCTA 60.105 44.000 0.00 0.00 36.85 2.94
2483 3202 4.705507 TCAGTTATCCTACTTCGCACTCTT 59.294 41.667 0.00 0.00 0.00 2.85
2498 3217 3.393800 CACTCTTGCCGATGGTTATAGG 58.606 50.000 0.00 0.00 32.71 2.57
2500 3219 4.038763 CACTCTTGCCGATGGTTATAGGTA 59.961 45.833 0.00 0.00 32.21 3.08
2504 3223 4.330944 TGCCGATGGTTATAGGTAGTTG 57.669 45.455 0.00 0.00 32.21 3.16
2510 3229 6.342906 CGATGGTTATAGGTAGTTGGTTTCA 58.657 40.000 0.00 0.00 0.00 2.69
2514 3233 7.924541 TGGTTATAGGTAGTTGGTTTCATCTT 58.075 34.615 0.00 0.00 0.00 2.40
2535 3254 2.756760 TCAATCCTGATTTTGCTGAGGC 59.243 45.455 0.00 0.00 39.26 4.70
2537 3256 1.138247 CCTGATTTTGCTGAGGCGC 59.862 57.895 0.00 0.00 42.25 6.53
2549 3268 3.193267 TGCTGAGGCGCTCATTTTTAATT 59.807 39.130 7.64 0.00 39.92 1.40
2555 3274 6.127647 TGAGGCGCTCATTTTTAATTCAGATT 60.128 34.615 7.64 0.00 35.39 2.40
2597 3316 8.561738 AATCATAAGTTGTTCATTAAGGTCGT 57.438 30.769 0.00 0.00 0.00 4.34
2605 3324 7.879160 AGTTGTTCATTAAGGTCGTACCATAAA 59.121 33.333 6.78 0.00 41.95 1.40
2657 3379 8.773404 ACTAACACCATGTTTAGATTCTACAC 57.227 34.615 11.14 3.49 41.45 2.90
2806 3529 8.233190 CCTGCTAAAGTGAAAATCTGACTTAAG 58.767 37.037 0.00 0.00 29.71 1.85
2827 3550 8.986477 TTAAGACTAGTTTACGGGTTGATTAC 57.014 34.615 0.00 0.00 0.00 1.89
2830 3553 6.024552 ACTAGTTTACGGGTTGATTACGAA 57.975 37.500 0.00 0.00 0.00 3.85
2837 3560 9.213819 GTTTACGGGTTGATTACGAAAAATATC 57.786 33.333 0.00 0.00 0.00 1.63
2883 3606 8.490355 CAAAAATCTGACTTAAAGTTGGATTGC 58.510 33.333 0.00 0.00 33.46 3.56
2906 3629 7.821652 TGCGGTTTAATTATCAGAAACATCAA 58.178 30.769 3.82 0.00 35.26 2.57
2907 3630 7.967854 TGCGGTTTAATTATCAGAAACATCAAG 59.032 33.333 3.82 0.00 35.26 3.02
2908 3631 7.432252 GCGGTTTAATTATCAGAAACATCAAGG 59.568 37.037 3.82 0.00 35.26 3.61
2909 3632 8.673711 CGGTTTAATTATCAGAAACATCAAGGA 58.326 33.333 3.82 0.00 35.26 3.36
2916 3639 8.924511 TTATCAGAAACATCAAGGAGTTTTCT 57.075 30.769 0.00 0.00 38.01 2.52
2993 3717 7.891183 CACTATATAGTGTGTGAATAAGGGC 57.109 40.000 27.86 0.00 46.51 5.19
2994 3718 6.874134 CACTATATAGTGTGTGAATAAGGGCC 59.126 42.308 27.86 0.00 46.51 5.80
2995 3719 6.787957 ACTATATAGTGTGTGAATAAGGGCCT 59.212 38.462 14.71 0.00 34.72 5.19
2996 3720 2.789409 AGTGTGTGAATAAGGGCCTC 57.211 50.000 6.46 0.00 0.00 4.70
2997 3721 2.269940 AGTGTGTGAATAAGGGCCTCT 58.730 47.619 6.46 0.00 0.00 3.69
2998 3722 3.450904 AGTGTGTGAATAAGGGCCTCTA 58.549 45.455 6.46 1.82 0.00 2.43
2999 3723 4.040755 AGTGTGTGAATAAGGGCCTCTAT 58.959 43.478 6.46 4.41 0.00 1.98
3000 3724 4.130118 GTGTGTGAATAAGGGCCTCTATG 58.870 47.826 6.46 0.00 0.00 2.23
3001 3725 4.037222 TGTGTGAATAAGGGCCTCTATGA 58.963 43.478 6.46 0.00 0.00 2.15
3002 3726 4.660303 TGTGTGAATAAGGGCCTCTATGAT 59.340 41.667 6.46 0.00 0.00 2.45
3003 3727 5.132648 TGTGTGAATAAGGGCCTCTATGATT 59.867 40.000 6.46 1.73 0.00 2.57
3004 3728 5.703130 GTGTGAATAAGGGCCTCTATGATTC 59.297 44.000 6.46 11.61 0.00 2.52
3005 3729 4.932200 GTGAATAAGGGCCTCTATGATTCG 59.068 45.833 6.46 0.00 0.00 3.34
3006 3730 3.618690 ATAAGGGCCTCTATGATTCGC 57.381 47.619 6.46 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 95 1.966451 AGAGCGCTCCCCAAAAACG 60.966 57.895 32.94 0.00 0.00 3.60
127 131 2.126071 CGGTGTCCGCGATGAACT 60.126 61.111 8.23 0.00 41.17 3.01
155 168 0.316204 GGAAGAAGTCGTCGTTGGGA 59.684 55.000 0.00 0.00 0.00 4.37
204 217 1.033574 GGGTCGACATCCTCACTAGG 58.966 60.000 18.91 0.00 45.21 3.02
209 222 0.895530 GACTTGGGTCGACATCCTCA 59.104 55.000 18.91 4.42 32.47 3.86
229 243 2.125188 GCAGGAGCAGGAGCACTC 60.125 66.667 0.00 0.00 45.49 3.51
272 287 6.198639 ACTGTGATAGGACCTCTAACAGAAT 58.801 40.000 24.76 6.55 38.30 2.40
353 368 7.213216 ACATATCTAGAGCAGACAGTACATG 57.787 40.000 0.00 0.00 35.62 3.21
354 369 7.831691 AACATATCTAGAGCAGACAGTACAT 57.168 36.000 0.00 0.00 35.62 2.29
499 536 7.894364 ACAGAGGGAGTAAGTATGAAAACTCTA 59.106 37.037 0.00 0.00 31.09 2.43
576 616 6.784068 AATTAAAACGAGTGAACAAACACG 57.216 33.333 0.00 0.00 44.35 4.49
602 642 2.036862 ACACTCCCTCCGTTCACTTTAC 59.963 50.000 0.00 0.00 0.00 2.01
645 686 9.974980 TTTTAAGCAACCCTACAAAGAAAATAG 57.025 29.630 0.00 0.00 0.00 1.73
704 745 9.855021 GTAGCCAATATTTTGACTATTGTTTGT 57.145 29.630 0.00 0.00 35.65 2.83
761 808 1.486726 GATCGGGGATTCAAGACTGGT 59.513 52.381 0.00 0.00 0.00 4.00
764 811 1.765314 CTGGATCGGGGATTCAAGACT 59.235 52.381 0.00 0.00 25.83 3.24
945 992 2.438614 CTGGCGAGAGGAGACGGA 60.439 66.667 0.00 0.00 0.00 4.69
1223 1270 4.035102 GAGGTGGGTGGGTGGAGC 62.035 72.222 0.00 0.00 0.00 4.70
1240 1287 4.292178 GAGAGGGGAGCGATGCGG 62.292 72.222 0.00 0.00 0.00 5.69
1241 1288 3.206211 GAGAGAGGGGAGCGATGCG 62.206 68.421 0.00 0.00 0.00 4.73
1242 1289 2.733945 GAGAGAGGGGAGCGATGC 59.266 66.667 0.00 0.00 0.00 3.91
1243 1290 2.560119 CGGAGAGAGGGGAGCGATG 61.560 68.421 0.00 0.00 0.00 3.84
1244 1291 2.203422 CGGAGAGAGGGGAGCGAT 60.203 66.667 0.00 0.00 0.00 4.58
1245 1292 4.507916 CCGGAGAGAGGGGAGCGA 62.508 72.222 0.00 0.00 0.00 4.93
1247 1294 3.438615 TAGCCGGAGAGAGGGGAGC 62.439 68.421 5.05 0.00 0.00 4.70
1248 1295 1.228429 CTAGCCGGAGAGAGGGGAG 60.228 68.421 5.05 0.00 0.00 4.30
1249 1296 1.581923 AACTAGCCGGAGAGAGGGGA 61.582 60.000 5.05 0.00 0.00 4.81
1250 1297 1.075896 AACTAGCCGGAGAGAGGGG 60.076 63.158 5.05 0.00 0.00 4.79
1251 1298 1.448922 CGAACTAGCCGGAGAGAGGG 61.449 65.000 5.05 0.00 0.00 4.30
1252 1299 2.026522 CGAACTAGCCGGAGAGAGG 58.973 63.158 5.05 0.00 0.00 3.69
1302 1352 2.089980 CTTCCTGAATCCCTGCACAAG 58.910 52.381 0.00 0.00 0.00 3.16
1688 1738 1.229529 GTCCTCCTCCCCCACTTCA 60.230 63.158 0.00 0.00 0.00 3.02
1742 1792 2.050351 CCTATCGCGACGCCGAAT 60.050 61.111 12.93 8.17 41.01 3.34
1763 1813 3.127352 ATCCTCGCGCGACCTCTTC 62.127 63.158 31.40 0.00 0.00 2.87
1804 1854 0.332972 GTCCTCCTCTGCCCCATTTT 59.667 55.000 0.00 0.00 0.00 1.82
1835 1885 0.390472 CGTGTTCTTGCTCCTCCTCC 60.390 60.000 0.00 0.00 0.00 4.30
1906 1962 3.210528 GATCCGACCGCTCCGTCT 61.211 66.667 0.00 0.00 0.00 4.18
1976 2032 2.716244 CTACGATCACGCGAGCCT 59.284 61.111 15.93 0.00 43.96 4.58
2060 2129 1.153745 CGAGCTAGAGTGGTGCACC 60.154 63.158 29.67 29.67 34.49 5.01
2064 2133 2.871182 TAATGCGAGCTAGAGTGGTG 57.129 50.000 0.00 0.00 0.00 4.17
2146 2215 0.511221 CGGTTGTTCTACACGCCTTG 59.489 55.000 0.00 0.00 0.00 3.61
2150 2219 1.068333 TCTACCGGTTGTTCTACACGC 60.068 52.381 15.04 0.00 0.00 5.34
2152 2221 4.563061 ACAATCTACCGGTTGTTCTACAC 58.437 43.478 15.04 0.00 35.13 2.90
2164 2527 5.114081 CCCTAACTACCAAACAATCTACCG 58.886 45.833 0.00 0.00 0.00 4.02
2196 2559 5.368989 CCAATCCTAGGTCTACATGGAAAC 58.631 45.833 9.08 0.00 0.00 2.78
2215 2578 5.644188 TCCAACTCTTCTCATTTTCCCAAT 58.356 37.500 0.00 0.00 0.00 3.16
2233 2596 4.470334 ACAATAAACCATGGCATCCAAC 57.530 40.909 13.04 0.00 36.95 3.77
2264 2634 5.182487 ACAACCTTGGCCTTTTTACAAAAG 58.818 37.500 3.32 2.50 0.00 2.27
2270 2640 8.252624 ACTTAAATACAACCTTGGCCTTTTTA 57.747 30.769 3.32 0.00 0.00 1.52
2285 2655 8.322828 TCTATGGGTTTGTGCTACTTAAATACA 58.677 33.333 0.00 0.00 0.00 2.29
2286 2656 8.726870 TCTATGGGTTTGTGCTACTTAAATAC 57.273 34.615 0.00 0.00 0.00 1.89
2335 2707 0.595588 TTCCGTTGCATCGCACAAAT 59.404 45.000 11.68 0.00 38.71 2.32
2337 2709 0.882484 TCTTCCGTTGCATCGCACAA 60.882 50.000 11.68 3.50 38.71 3.33
2339 2711 0.237235 TTTCTTCCGTTGCATCGCAC 59.763 50.000 11.68 0.00 38.71 5.34
2363 3082 7.878644 GGGTTAGAAGAGTGAGAATGTAAGTTT 59.121 37.037 0.00 0.00 0.00 2.66
2365 3084 6.497259 TGGGTTAGAAGAGTGAGAATGTAAGT 59.503 38.462 0.00 0.00 0.00 2.24
2367 3086 6.928348 TGGGTTAGAAGAGTGAGAATGTAA 57.072 37.500 0.00 0.00 0.00 2.41
2368 3087 6.928348 TTGGGTTAGAAGAGTGAGAATGTA 57.072 37.500 0.00 0.00 0.00 2.29
2369 3088 5.825593 TTGGGTTAGAAGAGTGAGAATGT 57.174 39.130 0.00 0.00 0.00 2.71
2370 3089 8.970859 ATTATTGGGTTAGAAGAGTGAGAATG 57.029 34.615 0.00 0.00 0.00 2.67
2371 3090 8.772250 TGATTATTGGGTTAGAAGAGTGAGAAT 58.228 33.333 0.00 0.00 0.00 2.40
2372 3091 8.146053 TGATTATTGGGTTAGAAGAGTGAGAA 57.854 34.615 0.00 0.00 0.00 2.87
2373 3092 7.733773 TGATTATTGGGTTAGAAGAGTGAGA 57.266 36.000 0.00 0.00 0.00 3.27
2374 3093 8.206867 TCATGATTATTGGGTTAGAAGAGTGAG 58.793 37.037 0.00 0.00 0.00 3.51
2375 3094 7.987458 GTCATGATTATTGGGTTAGAAGAGTGA 59.013 37.037 0.00 0.00 0.00 3.41
2425 3144 7.786030 TGGGATGTCATGTGTTTAAAGAAAAA 58.214 30.769 0.00 0.00 0.00 1.94
2426 3145 7.353414 TGGGATGTCATGTGTTTAAAGAAAA 57.647 32.000 0.00 0.00 0.00 2.29
2434 3153 3.760151 CACAGATGGGATGTCATGTGTTT 59.240 43.478 5.13 0.00 45.44 2.83
2483 3202 3.070446 CCAACTACCTATAACCATCGGCA 59.930 47.826 0.00 0.00 0.00 5.69
2498 3217 6.655003 TCAGGATTGAAGATGAAACCAACTAC 59.345 38.462 0.00 0.00 0.00 2.73
2500 3219 5.634118 TCAGGATTGAAGATGAAACCAACT 58.366 37.500 0.00 0.00 0.00 3.16
2504 3223 6.312180 GCAAAATCAGGATTGAAGATGAAACC 59.688 38.462 0.00 0.00 36.78 3.27
2510 3229 5.360144 CCTCAGCAAAATCAGGATTGAAGAT 59.640 40.000 0.00 0.00 36.78 2.40
2514 3233 2.756760 GCCTCAGCAAAATCAGGATTGA 59.243 45.455 0.00 0.00 39.53 2.57
2535 3254 8.961092 CATACCAATCTGAATTAAAAATGAGCG 58.039 33.333 0.00 0.00 0.00 5.03
2571 3290 9.661563 ACGACCTTAATGAACAACTTATGATTA 57.338 29.630 0.00 0.00 0.00 1.75
2578 3297 5.613329 TGGTACGACCTTAATGAACAACTT 58.387 37.500 0.00 0.00 39.58 2.66
2579 3298 5.217978 TGGTACGACCTTAATGAACAACT 57.782 39.130 0.00 0.00 39.58 3.16
2633 3355 8.771920 TGTGTAGAATCTAAACATGGTGTTAG 57.228 34.615 9.13 2.37 40.14 2.34
2773 3495 2.178912 TCACTTTAGCAGGAAACCCG 57.821 50.000 0.00 0.00 0.00 5.28
2806 3529 5.640732 TCGTAATCAACCCGTAAACTAGTC 58.359 41.667 0.00 0.00 0.00 2.59
2810 3533 6.616774 TTTTTCGTAATCAACCCGTAAACT 57.383 33.333 0.00 0.00 0.00 2.66
2815 3538 6.037830 CCTGATATTTTTCGTAATCAACCCGT 59.962 38.462 0.00 0.00 0.00 5.28
2866 3589 4.499037 AACCGCAATCCAACTTTAAGTC 57.501 40.909 0.00 0.00 0.00 3.01
2874 3597 6.791303 TCTGATAATTAAACCGCAATCCAAC 58.209 36.000 0.00 0.00 0.00 3.77
2883 3606 8.673711 TCCTTGATGTTTCTGATAATTAAACCG 58.326 33.333 0.00 0.00 33.21 4.44
2971 3695 7.179338 AGAGGCCCTTATTCACACACTATATAG 59.821 40.741 8.27 8.27 0.00 1.31
2986 3710 3.618690 GCGAATCATAGAGGCCCTTAT 57.381 47.619 0.00 0.00 0.00 1.73



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

AutoCloner maintained by Alex Coulton.