Multiple sequence alignment - TraesCS6A01G217100

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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 TraesCS6A01G217100 chr6A 100.000 3008 0 0 1 3008 399720992 399723999 0.000000e+00 5555
1 TraesCS6A01G217100 chr6B 93.650 1874 59 22 384 2210 438387554 438385694 0.000000e+00 2747
2 TraesCS6A01G217100 chr6B 89.723 759 60 15 2254 3007 438385691 438384946 0.000000e+00 953
3 TraesCS6A01G217100 chr6B 92.614 176 13 0 11 186 438387965 438387790 1.380000e-63 254
4 TraesCS6A01G217100 chr6B 81.338 284 41 10 2197 2477 88656821 88657095 1.400000e-53 220
5 TraesCS6A01G217100 chr6B 91.262 103 6 2 205 304 438387653 438387551 1.450000e-28 137
6 TraesCS6A01G217100 chr6B 91.667 96 7 1 294 388 688799801 688799896 6.770000e-27 132
7 TraesCS6A01G217100 chr6D 94.698 1207 50 8 993 2192 276456895 276455696 0.000000e+00 1862
8 TraesCS6A01G217100 chr6D 94.737 608 23 5 384 990 276457528 276456929 0.000000e+00 937
9 TraesCS6A01G217100 chr6D 86.184 152 8 6 129 267 276457699 276457548 5.190000e-33 152
10 TraesCS6A01G217100 chr6D 92.473 93 6 1 1 93 276457784 276457693 6.770000e-27 132
11 TraesCS6A01G217100 chr3B 85.204 1007 83 35 1112 2092 766631395 766632361 0.000000e+00 974
12 TraesCS6A01G217100 chr3B 81.135 1198 135 47 992 2130 769056382 769055217 0.000000e+00 876
13 TraesCS6A01G217100 chr3B 79.643 673 103 18 2310 2975 169333216 169333861 1.270000e-123 453
14 TraesCS6A01G217100 chr3D 86.504 904 77 23 1112 2005 575726002 575726870 0.000000e+00 952
15 TraesCS6A01G217100 chr3D 83.871 899 102 22 1117 2005 577255708 577254843 0.000000e+00 817
16 TraesCS6A01G217100 chr3D 87.250 400 36 8 1399 1790 577264253 577263861 2.750000e-120 442
17 TraesCS6A01G217100 chr3D 81.452 372 47 14 2179 2542 611251601 611251244 4.910000e-73 285
18 TraesCS6A01G217100 chr3D 94.186 86 5 0 303 388 112210175 112210090 6.770000e-27 132
19 TraesCS6A01G217100 chr3D 93.103 87 6 0 301 387 267110518 267110604 8.750000e-26 128
20 TraesCS6A01G217100 chr3D 76.860 242 28 14 1911 2129 577263863 577263627 8.810000e-21 111
21 TraesCS6A01G217100 chr3A 84.251 1035 98 32 1112 2121 711217972 711218966 0.000000e+00 948
22 TraesCS6A01G217100 chr3A 83.300 1000 100 36 1145 2117 711203124 711204083 0.000000e+00 859
23 TraesCS6A01G217100 chr3A 81.818 572 64 20 1117 1670 712572341 712571792 7.650000e-121 444
24 TraesCS6A01G217100 chr3A 79.469 414 71 14 2180 2586 679751303 679751709 6.350000e-72 281
25 TraesCS6A01G217100 chr3A 81.443 291 44 9 2191 2476 9974124 9973839 2.330000e-56 230
26 TraesCS6A01G217100 chr5D 88.116 345 35 4 1664 2005 91405841 91405500 3.610000e-109 405
27 TraesCS6A01G217100 chr5D 82.701 422 65 8 2591 3008 371059613 371060030 4.740000e-98 368
28 TraesCS6A01G217100 chr5D 83.805 389 42 15 2632 3008 449947740 449947361 1.720000e-92 350
29 TraesCS6A01G217100 chr5D 81.352 429 56 16 2590 3008 312479598 312479184 8.040000e-86 327
30 TraesCS6A01G217100 chr5D 79.104 402 53 17 2190 2586 268692168 268691793 6.440000e-62 248
31 TraesCS6A01G217100 chr5D 93.023 86 6 0 303 388 336723442 336723527 3.150000e-25 126
32 TraesCS6A01G217100 chr5A 87.826 345 36 4 1664 2005 85164426 85164085 1.680000e-107 399
33 TraesCS6A01G217100 chr7D 85.677 384 39 13 2631 3008 490439317 490439690 1.010000e-104 390
34 TraesCS6A01G217100 chr7D 94.186 86 5 0 303 388 509611651 509611736 6.770000e-27 132
35 TraesCS6A01G217100 chr2D 83.607 427 56 11 2590 3008 488215859 488216279 3.640000e-104 388
36 TraesCS6A01G217100 chr2D 81.860 430 61 14 2583 3008 189841385 189841801 2.220000e-91 346
37 TraesCS6A01G217100 chr2D 83.152 368 52 8 2223 2586 55317579 55317940 8.040000e-86 327
38 TraesCS6A01G217100 chr5B 86.957 345 39 4 1664 2005 96764631 96764290 1.690000e-102 383
39 TraesCS6A01G217100 chr5B 81.871 342 57 5 2233 2572 322558150 322558488 1.770000e-72 283
40 TraesCS6A01G217100 chr4A 81.882 425 62 12 2591 3008 467154078 467154494 7.980000e-91 344
41 TraesCS6A01G217100 chr1D 81.690 426 53 18 2590 3006 442153871 442153462 6.220000e-87 331
42 TraesCS6A01G217100 chr2B 79.707 409 68 9 2190 2587 755339587 755339991 6.350000e-72 281
43 TraesCS6A01G217100 chr4D 79.592 343 61 8 1664 2000 508501908 508502247 1.390000e-58 237
44 TraesCS6A01G217100 chr4D 94.253 87 5 0 301 387 337701286 337701200 1.880000e-27 134
45 TraesCS6A01G217100 chr4D 93.103 87 6 0 301 387 50297643 50297729 8.750000e-26 128
46 TraesCS6A01G217100 chr4D 93.103 87 6 0 301 387 329882936 329883022 8.750000e-26 128
47 TraesCS6A01G217100 chr1A 95.294 85 4 0 303 387 9547047 9546963 5.230000e-28 135


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 TraesCS6A01G217100 chr6A 399720992 399723999 3007 False 5555.00 5555 100.00000 1 3008 1 chr6A.!!$F1 3007
1 TraesCS6A01G217100 chr6B 438384946 438387965 3019 True 1022.75 2747 91.81225 11 3007 4 chr6B.!!$R1 2996
2 TraesCS6A01G217100 chr6D 276455696 276457784 2088 True 770.75 1862 92.02300 1 2192 4 chr6D.!!$R1 2191
3 TraesCS6A01G217100 chr3B 766631395 766632361 966 False 974.00 974 85.20400 1112 2092 1 chr3B.!!$F2 980
4 TraesCS6A01G217100 chr3B 769055217 769056382 1165 True 876.00 876 81.13500 992 2130 1 chr3B.!!$R1 1138
5 TraesCS6A01G217100 chr3B 169333216 169333861 645 False 453.00 453 79.64300 2310 2975 1 chr3B.!!$F1 665
6 TraesCS6A01G217100 chr3D 575726002 575726870 868 False 952.00 952 86.50400 1112 2005 1 chr3D.!!$F2 893
7 TraesCS6A01G217100 chr3D 577254843 577255708 865 True 817.00 817 83.87100 1117 2005 1 chr3D.!!$R2 888
8 TraesCS6A01G217100 chr3D 577263627 577264253 626 True 276.50 442 82.05500 1399 2129 2 chr3D.!!$R4 730
9 TraesCS6A01G217100 chr3A 711217972 711218966 994 False 948.00 948 84.25100 1112 2121 1 chr3A.!!$F3 1009
10 TraesCS6A01G217100 chr3A 711203124 711204083 959 False 859.00 859 83.30000 1145 2117 1 chr3A.!!$F2 972
11 TraesCS6A01G217100 chr3A 712571792 712572341 549 True 444.00 444 81.81800 1117 1670 1 chr3A.!!$R2 553

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
703 835 0.45339 GGAAGCACCTGTAATGCAGC 59.547 55.0 0.0 0.0 45.92 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2056 2324 1.202154 GCGACGTCTCAGCTAGCTTAA 60.202 52.381 16.46 5.38 0.0 1.85 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
23 25 3.054878 ACGTTCGTCGCTTATGACTTTT 58.945 40.909 0.00 0.00 44.19 2.27
26 28 4.375606 CGTTCGTCGCTTATGACTTTTCAA 60.376 41.667 0.00 0.00 36.71 2.69
34 36 7.220108 GTCGCTTATGACTTTTCAACTTTTTGT 59.780 33.333 0.00 0.00 34.61 2.83
36 38 8.469125 CGCTTATGACTTTTCAACTTTTTGTAC 58.531 33.333 0.00 0.00 34.61 2.90
105 107 9.753674 TTCAAGGATTAATACCACAAAGAAGAT 57.246 29.630 0.00 0.00 0.00 2.40
161 163 6.725246 TGCAAGAGCTACTTTGTAGTTTTTC 58.275 36.000 6.60 1.51 42.74 2.29
238 360 8.990163 TTAAAGGAAAAGGTGAACTGACTATT 57.010 30.769 0.00 0.00 0.00 1.73
269 393 6.093495 TCCAACATTGTATCTTTCGATGTTCC 59.907 38.462 8.11 0.00 43.67 3.62
304 429 7.617528 GCTGATATTTCGATGCTTCGTTAGTAC 60.618 40.741 19.92 10.52 45.65 2.73
305 430 7.423199 TGATATTTCGATGCTTCGTTAGTACT 58.577 34.615 19.92 0.00 45.65 2.73
306 431 7.590322 TGATATTTCGATGCTTCGTTAGTACTC 59.410 37.037 19.92 10.71 45.65 2.59
307 432 3.687572 TCGATGCTTCGTTAGTACTCC 57.312 47.619 19.92 0.00 45.65 3.85
308 433 2.357009 TCGATGCTTCGTTAGTACTCCC 59.643 50.000 19.92 0.00 45.65 4.30
309 434 2.358267 CGATGCTTCGTTAGTACTCCCT 59.642 50.000 13.46 0.00 40.53 4.20
310 435 3.548415 CGATGCTTCGTTAGTACTCCCTC 60.548 52.174 13.46 0.00 40.53 4.30
311 436 3.083122 TGCTTCGTTAGTACTCCCTCT 57.917 47.619 0.00 0.00 0.00 3.69
312 437 4.226427 TGCTTCGTTAGTACTCCCTCTA 57.774 45.455 0.00 0.00 0.00 2.43
313 438 4.789807 TGCTTCGTTAGTACTCCCTCTAT 58.210 43.478 0.00 0.00 0.00 1.98
314 439 4.820716 TGCTTCGTTAGTACTCCCTCTATC 59.179 45.833 0.00 0.00 0.00 2.08
315 440 4.216042 GCTTCGTTAGTACTCCCTCTATCC 59.784 50.000 0.00 0.00 0.00 2.59
316 441 4.363991 TCGTTAGTACTCCCTCTATCCC 57.636 50.000 0.00 0.00 0.00 3.85
317 442 3.718434 TCGTTAGTACTCCCTCTATCCCA 59.282 47.826 0.00 0.00 0.00 4.37
318 443 4.166725 TCGTTAGTACTCCCTCTATCCCAA 59.833 45.833 0.00 0.00 0.00 4.12
319 444 4.891756 CGTTAGTACTCCCTCTATCCCAAA 59.108 45.833 0.00 0.00 0.00 3.28
320 445 5.361857 CGTTAGTACTCCCTCTATCCCAAAA 59.638 44.000 0.00 0.00 0.00 2.44
321 446 6.041751 CGTTAGTACTCCCTCTATCCCAAAAT 59.958 42.308 0.00 0.00 0.00 1.82
322 447 7.232127 CGTTAGTACTCCCTCTATCCCAAAATA 59.768 40.741 0.00 0.00 0.00 1.40
323 448 9.102453 GTTAGTACTCCCTCTATCCCAAAATAT 57.898 37.037 0.00 0.00 0.00 1.28
326 451 9.327731 AGTACTCCCTCTATCCCAAAATATAAG 57.672 37.037 0.00 0.00 0.00 1.73
327 452 9.322769 GTACTCCCTCTATCCCAAAATATAAGA 57.677 37.037 0.00 0.00 0.00 2.10
328 453 8.814448 ACTCCCTCTATCCCAAAATATAAGAA 57.186 34.615 0.00 0.00 0.00 2.52
329 454 8.661345 ACTCCCTCTATCCCAAAATATAAGAAC 58.339 37.037 0.00 0.00 0.00 3.01
330 455 7.676947 TCCCTCTATCCCAAAATATAAGAACG 58.323 38.462 0.00 0.00 0.00 3.95
331 456 7.291651 TCCCTCTATCCCAAAATATAAGAACGT 59.708 37.037 0.00 0.00 0.00 3.99
332 457 7.937394 CCCTCTATCCCAAAATATAAGAACGTT 59.063 37.037 0.00 0.00 0.00 3.99
333 458 9.338622 CCTCTATCCCAAAATATAAGAACGTTT 57.661 33.333 0.46 0.00 0.00 3.60
351 476 9.971922 AGAACGTTTTTAATACTACACTACTGT 57.028 29.630 0.46 0.00 0.00 3.55
353 478 9.748708 AACGTTTTTAATACTACACTACTGTCA 57.251 29.630 0.00 0.00 0.00 3.58
354 479 9.748708 ACGTTTTTAATACTACACTACTGTCAA 57.251 29.630 0.00 0.00 0.00 3.18
363 488 9.998106 ATACTACACTACTGTCAAAAATGTTCT 57.002 29.630 0.00 0.00 0.00 3.01
364 489 8.732746 ACTACACTACTGTCAAAAATGTTCTT 57.267 30.769 0.00 0.00 0.00 2.52
365 490 9.826574 ACTACACTACTGTCAAAAATGTTCTTA 57.173 29.630 0.00 0.00 0.00 2.10
381 506 8.940397 AATGTTCTTATATTATGGGACCAAGG 57.060 34.615 0.00 0.00 0.00 3.61
382 507 6.848069 TGTTCTTATATTATGGGACCAAGGG 58.152 40.000 0.00 0.00 0.00 3.95
383 508 6.621931 TGTTCTTATATTATGGGACCAAGGGA 59.378 38.462 0.00 0.00 0.00 4.20
384 509 6.952605 TCTTATATTATGGGACCAAGGGAG 57.047 41.667 0.00 0.00 0.00 4.30
385 510 6.399013 TCTTATATTATGGGACCAAGGGAGT 58.601 40.000 0.00 0.00 0.00 3.85
386 511 7.550042 TCTTATATTATGGGACCAAGGGAGTA 58.450 38.462 0.00 0.00 0.00 2.59
447 572 6.442112 GGTATCTTGTACGTAACCACTATCC 58.558 44.000 0.00 0.00 0.00 2.59
476 601 1.065647 ATCATGCCCTGATCCTCTGG 58.934 55.000 0.00 0.00 40.77 3.86
541 666 4.092816 GTTTGGTATTTTCGCGGTACATG 58.907 43.478 6.13 0.00 0.00 3.21
544 669 4.193090 TGGTATTTTCGCGGTACATGAAT 58.807 39.130 6.13 0.00 0.00 2.57
574 699 0.798776 GTCACTGATTGCAAGACGGG 59.201 55.000 4.94 0.00 0.00 5.28
635 767 4.202090 GCCAAGAAAAAGATGCCTCTATGG 60.202 45.833 0.00 0.00 39.35 2.74
703 835 0.453390 GGAAGCACCTGTAATGCAGC 59.547 55.000 0.00 0.00 45.92 5.25
877 1009 0.657840 CCGTTCATTCATTCCCTCGC 59.342 55.000 0.00 0.00 0.00 5.03
957 1089 1.070843 CGGCCTATAAATTCACACGCG 60.071 52.381 3.53 3.53 0.00 6.01
958 1090 1.333791 GGCCTATAAATTCACACGCGC 60.334 52.381 5.73 0.00 0.00 6.86
959 1091 1.333791 GCCTATAAATTCACACGCGCC 60.334 52.381 5.73 0.00 0.00 6.53
987 1119 2.756760 ACTGCATCAAGCCATTAACCAG 59.243 45.455 0.00 0.00 44.83 4.00
990 1122 2.094078 GCATCAAGCCATTAACCAGCAA 60.094 45.455 0.00 0.00 37.23 3.91
995 1158 1.969923 AGCCATTAACCAGCAAAAGCA 59.030 42.857 0.00 0.00 0.00 3.91
1043 1209 0.667792 GTTGCGGTCGCTCTCTTCTT 60.668 55.000 16.36 0.00 42.51 2.52
1440 1644 4.543692 TGTCGTTTCGTTTGTTTTTCCAA 58.456 34.783 0.00 0.00 0.00 3.53
1659 1897 2.838386 GCATCATCGACATGCAGTTT 57.162 45.000 21.06 0.00 45.19 2.66
1854 2092 1.381327 GATGAGGGAGTCGTGGGGA 60.381 63.158 0.00 0.00 0.00 4.81
1902 2140 2.442413 CTGCAGGGGCCCTTTTCT 59.558 61.111 26.34 7.18 40.13 2.52
2054 2322 1.376683 GCATGGGTTAGTCGTGCCA 60.377 57.895 0.00 0.00 40.24 4.92
2055 2323 0.958382 GCATGGGTTAGTCGTGCCAA 60.958 55.000 0.00 0.00 40.24 4.52
2056 2324 1.750193 CATGGGTTAGTCGTGCCAAT 58.250 50.000 0.00 0.00 0.00 3.16
2156 2439 5.277154 GCGCATACGTTTTTCATGGTATACT 60.277 40.000 0.30 0.00 42.83 2.12
2164 2447 6.309494 CGTTTTTCATGGTATACTTGTCTCGA 59.691 38.462 2.25 0.00 0.00 4.04
2165 2448 7.148705 CGTTTTTCATGGTATACTTGTCTCGAA 60.149 37.037 2.25 0.00 0.00 3.71
2202 2487 3.992943 TTTTAGCTACTAGCAAGGGCA 57.007 42.857 10.73 0.00 45.56 5.36
2207 2492 1.407437 GCTACTAGCAAGGGCATGTGT 60.407 52.381 2.96 0.00 44.61 3.72
2210 2495 1.202927 ACTAGCAAGGGCATGTGTGTT 60.203 47.619 0.00 0.00 44.61 3.32
2211 2496 1.200716 CTAGCAAGGGCATGTGTGTTG 59.799 52.381 0.00 0.00 44.61 3.33
2212 2497 1.665599 GCAAGGGCATGTGTGTTGC 60.666 57.895 7.96 7.96 40.72 4.17
2213 2498 1.740905 CAAGGGCATGTGTGTTGCA 59.259 52.632 0.00 0.00 41.95 4.08
2214 2499 0.104487 CAAGGGCATGTGTGTTGCAA 59.896 50.000 0.00 0.00 41.95 4.08
2215 2500 0.104671 AAGGGCATGTGTGTTGCAAC 59.895 50.000 22.83 22.83 41.95 4.17
2216 2501 1.661197 GGGCATGTGTGTTGCAACG 60.661 57.895 23.79 10.03 41.95 4.10
2217 2502 1.065600 GGCATGTGTGTTGCAACGT 59.934 52.632 23.79 0.00 41.95 3.99
2218 2503 1.208009 GGCATGTGTGTTGCAACGTG 61.208 55.000 23.79 13.80 41.95 4.49
2219 2504 0.248417 GCATGTGTGTTGCAACGTGA 60.248 50.000 23.79 7.92 39.90 4.35
2220 2505 1.745566 CATGTGTGTTGCAACGTGAG 58.254 50.000 23.79 8.39 0.00 3.51
2221 2506 1.330213 CATGTGTGTTGCAACGTGAGA 59.670 47.619 23.79 9.51 0.00 3.27
2222 2507 1.443802 TGTGTGTTGCAACGTGAGAA 58.556 45.000 23.79 2.89 0.00 2.87
2223 2508 1.807142 TGTGTGTTGCAACGTGAGAAA 59.193 42.857 23.79 2.11 0.00 2.52
2224 2509 2.226674 TGTGTGTTGCAACGTGAGAAAA 59.773 40.909 23.79 1.33 0.00 2.29
2225 2510 3.238441 GTGTGTTGCAACGTGAGAAAAA 58.762 40.909 23.79 0.57 0.00 1.94
2288 2573 6.016360 GCATCACTGAGATACACTATCACTCT 60.016 42.308 0.00 0.00 37.65 3.24
2289 2574 7.584108 CATCACTGAGATACACTATCACTCTC 58.416 42.308 0.00 0.00 37.65 3.20
2522 2808 9.649167 ATTTTCTTGAATCCATGAACATTTCTC 57.351 29.630 0.00 0.00 36.55 2.87
2527 2813 7.395190 TGAATCCATGAACATTTCTCGAATT 57.605 32.000 0.00 0.00 0.00 2.17
2530 2816 9.956720 GAATCCATGAACATTTCTCGAATTAAT 57.043 29.630 0.00 0.00 0.00 1.40
2858 3150 7.846485 ACTATTTGCAACGTTTTTAATTGTGG 58.154 30.769 0.00 0.00 0.00 4.17
2864 3156 6.978659 TGCAACGTTTTTAATTGTGGACATTA 59.021 30.769 0.00 0.00 0.00 1.90
2895 3187 6.119144 TGTTTTTCTTGACTAGAGCAACAC 57.881 37.500 0.00 0.00 34.32 3.32
2919 3211 7.475565 CACTTCTAGAATCGACGAACATTTTTG 59.524 37.037 5.44 0.00 0.00 2.44
2994 3286 9.305110 GATTTAATGAACACTTTTTGAAATGCG 57.695 29.630 0.00 0.00 0.00 4.73
2999 3291 5.458452 TGAACACTTTTTGAAATGCGTGATC 59.542 36.000 8.17 6.81 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 25 6.912203 TGAATCACTCGTACAAAAAGTTGA 57.088 33.333 0.00 0.00 38.20 3.18
26 28 5.238650 CCCTTGAATCACTCGTACAAAAAGT 59.761 40.000 0.00 0.00 0.00 2.66
34 36 3.596214 GAAAGCCCTTGAATCACTCGTA 58.404 45.455 0.00 0.00 0.00 3.43
36 38 1.394917 CGAAAGCCCTTGAATCACTCG 59.605 52.381 0.00 0.00 0.00 4.18
218 340 9.614792 ATGTATAATAGTCAGTTCACCTTTTCC 57.385 33.333 0.00 0.00 0.00 3.13
304 429 7.819900 CGTTCTTATATTTTGGGATAGAGGGAG 59.180 40.741 0.00 0.00 0.00 4.30
305 430 7.291651 ACGTTCTTATATTTTGGGATAGAGGGA 59.708 37.037 0.00 0.00 0.00 4.20
306 431 7.450903 ACGTTCTTATATTTTGGGATAGAGGG 58.549 38.462 0.00 0.00 0.00 4.30
307 432 8.904099 AACGTTCTTATATTTTGGGATAGAGG 57.096 34.615 0.00 0.00 0.00 3.69
325 450 9.971922 ACAGTAGTGTAGTATTAAAAACGTTCT 57.028 29.630 0.00 0.00 34.05 3.01
327 452 9.748708 TGACAGTAGTGTAGTATTAAAAACGTT 57.251 29.630 2.39 0.00 36.88 3.99
328 453 9.748708 TTGACAGTAGTGTAGTATTAAAAACGT 57.251 29.630 2.39 0.00 36.88 3.99
337 462 9.998106 AGAACATTTTTGACAGTAGTGTAGTAT 57.002 29.630 2.39 0.00 36.88 2.12
338 463 9.826574 AAGAACATTTTTGACAGTAGTGTAGTA 57.173 29.630 2.39 0.00 36.88 1.82
339 464 8.732746 AAGAACATTTTTGACAGTAGTGTAGT 57.267 30.769 2.39 0.00 36.88 2.73
355 480 9.367160 CCTTGGTCCCATAATATAAGAACATTT 57.633 33.333 0.00 0.00 0.00 2.32
356 481 7.950124 CCCTTGGTCCCATAATATAAGAACATT 59.050 37.037 0.00 0.00 0.00 2.71
357 482 7.297108 TCCCTTGGTCCCATAATATAAGAACAT 59.703 37.037 0.00 0.00 0.00 2.71
358 483 6.621931 TCCCTTGGTCCCATAATATAAGAACA 59.378 38.462 0.00 0.00 0.00 3.18
359 484 7.086685 TCCCTTGGTCCCATAATATAAGAAC 57.913 40.000 0.00 0.00 0.00 3.01
360 485 6.855061 ACTCCCTTGGTCCCATAATATAAGAA 59.145 38.462 0.00 0.00 0.00 2.52
361 486 6.399013 ACTCCCTTGGTCCCATAATATAAGA 58.601 40.000 0.00 0.00 0.00 2.10
362 487 6.704056 ACTCCCTTGGTCCCATAATATAAG 57.296 41.667 0.00 0.00 0.00 1.73
363 488 7.742213 ACATACTCCCTTGGTCCCATAATATAA 59.258 37.037 0.00 0.00 0.00 0.98
364 489 7.260891 ACATACTCCCTTGGTCCCATAATATA 58.739 38.462 0.00 0.00 0.00 0.86
365 490 6.098446 ACATACTCCCTTGGTCCCATAATAT 58.902 40.000 0.00 0.00 0.00 1.28
366 491 5.482580 ACATACTCCCTTGGTCCCATAATA 58.517 41.667 0.00 0.00 0.00 0.98
367 492 4.315993 ACATACTCCCTTGGTCCCATAAT 58.684 43.478 0.00 0.00 0.00 1.28
368 493 3.714798 GACATACTCCCTTGGTCCCATAA 59.285 47.826 0.00 0.00 0.00 1.90
369 494 3.311028 TGACATACTCCCTTGGTCCCATA 60.311 47.826 0.00 0.00 0.00 2.74
370 495 2.127708 GACATACTCCCTTGGTCCCAT 58.872 52.381 0.00 0.00 0.00 4.00
371 496 1.203376 TGACATACTCCCTTGGTCCCA 60.203 52.381 0.00 0.00 0.00 4.37
372 497 1.209747 GTGACATACTCCCTTGGTCCC 59.790 57.143 0.00 0.00 0.00 4.46
373 498 2.093447 CAGTGACATACTCCCTTGGTCC 60.093 54.545 0.00 0.00 37.60 4.46
374 499 2.093447 CCAGTGACATACTCCCTTGGTC 60.093 54.545 0.00 0.00 37.60 4.02
375 500 1.909302 CCAGTGACATACTCCCTTGGT 59.091 52.381 0.00 0.00 37.60 3.67
376 501 2.187958 TCCAGTGACATACTCCCTTGG 58.812 52.381 0.00 0.00 37.60 3.61
377 502 4.651503 AGTATCCAGTGACATACTCCCTTG 59.348 45.833 8.27 0.00 37.60 3.61
378 503 4.884961 AGTATCCAGTGACATACTCCCTT 58.115 43.478 8.27 0.00 37.60 3.95
379 504 4.475345 GAGTATCCAGTGACATACTCCCT 58.525 47.826 21.03 2.89 42.94 4.20
380 505 3.253677 CGAGTATCCAGTGACATACTCCC 59.746 52.174 23.39 10.86 44.68 4.30
381 506 3.884091 ACGAGTATCCAGTGACATACTCC 59.116 47.826 23.39 13.51 44.68 3.85
382 507 4.335874 ACACGAGTATCCAGTGACATACTC 59.664 45.833 21.40 21.40 44.32 2.59
383 508 4.270834 ACACGAGTATCCAGTGACATACT 58.729 43.478 12.24 12.24 41.36 2.12
384 509 4.634184 ACACGAGTATCCAGTGACATAC 57.366 45.455 1.63 0.00 39.04 2.39
385 510 5.654603 AAACACGAGTATCCAGTGACATA 57.345 39.130 1.63 0.00 39.04 2.29
386 511 4.537135 AAACACGAGTATCCAGTGACAT 57.463 40.909 1.63 0.00 39.04 3.06
541 666 3.575630 TCAGTGACGAGCTTGTGTATTC 58.424 45.455 12.53 0.00 0.00 1.75
544 669 3.317150 CAATCAGTGACGAGCTTGTGTA 58.683 45.455 12.53 0.00 0.00 2.90
574 699 3.242413 CGTAGCAATTACAGCCACATGAC 60.242 47.826 0.00 0.00 32.27 3.06
828 960 0.911525 TGGAGAAAGGAGGAGCCAGG 60.912 60.000 0.00 0.00 40.02 4.45
877 1009 5.806654 TCAAATCAAAAGGAGGAAAAGGG 57.193 39.130 0.00 0.00 0.00 3.95
957 1089 1.880819 CTTGATGCAGTTGGTGGGGC 61.881 60.000 0.00 0.00 0.00 5.80
958 1090 1.880819 GCTTGATGCAGTTGGTGGGG 61.881 60.000 0.00 0.00 42.31 4.96
959 1091 1.588082 GCTTGATGCAGTTGGTGGG 59.412 57.895 0.00 0.00 42.31 4.61
987 1119 1.349259 CTGCCATCGCTTGCTTTTGC 61.349 55.000 0.00 0.00 40.27 3.68
990 1122 2.570181 GCTGCCATCGCTTGCTTT 59.430 55.556 0.00 0.00 34.11 3.51
1070 1236 1.043022 AGGCAGAAACCAAAAGCAGG 58.957 50.000 0.00 0.00 0.00 4.85
1317 1510 0.108804 CCTTGAAGAGCGGCTCGTTA 60.109 55.000 23.15 14.85 35.36 3.18
1440 1644 3.947612 ACAATCCAAGATCCATCAGCT 57.052 42.857 0.00 0.00 0.00 4.24
1513 1751 1.967066 GATGATCACCGTCTCAGGGAT 59.033 52.381 0.00 0.00 35.02 3.85
1659 1897 2.925706 TGGCACGGCACCCTCTTA 60.926 61.111 0.00 0.00 0.00 2.10
1854 2092 2.769621 TCCAGGCGCCAGATGGAT 60.770 61.111 27.24 3.90 38.19 3.41
1902 2140 3.220999 CTCGTTGGTGACCCGCAGA 62.221 63.158 0.00 0.00 0.00 4.26
2054 2322 3.696898 CGACGTCTCAGCTAGCTTAATT 58.303 45.455 16.46 0.00 0.00 1.40
2055 2323 2.541999 GCGACGTCTCAGCTAGCTTAAT 60.542 50.000 16.46 0.00 0.00 1.40
2056 2324 1.202154 GCGACGTCTCAGCTAGCTTAA 60.202 52.381 16.46 5.38 0.00 1.85
2202 2487 1.662517 TCTCACGTTGCAACACACAT 58.337 45.000 28.01 5.98 0.00 3.21
2244 2529 3.911868 TGCAGCAAAATGTGGTAATGAC 58.088 40.909 0.00 0.00 35.75 3.06
2245 2530 4.220163 TGATGCAGCAAAATGTGGTAATGA 59.780 37.500 0.00 0.00 35.75 2.57
2246 2531 4.327898 GTGATGCAGCAAAATGTGGTAATG 59.672 41.667 6.05 0.00 35.75 1.90
2247 2532 4.221262 AGTGATGCAGCAAAATGTGGTAAT 59.779 37.500 6.05 0.00 35.75 1.89
2248 2533 3.573538 AGTGATGCAGCAAAATGTGGTAA 59.426 39.130 6.05 0.00 35.75 2.85
2249 2534 3.057386 CAGTGATGCAGCAAAATGTGGTA 60.057 43.478 6.05 0.00 35.75 3.25
2250 2535 1.965643 AGTGATGCAGCAAAATGTGGT 59.034 42.857 6.05 0.00 38.97 4.16
2251 2536 2.029739 TCAGTGATGCAGCAAAATGTGG 60.030 45.455 6.05 0.00 0.00 4.17
2252 2537 3.057806 TCTCAGTGATGCAGCAAAATGTG 60.058 43.478 6.05 7.46 0.00 3.21
2356 2641 8.071122 TGGATTTGAAAAATGTTCACGATTTC 57.929 30.769 0.00 0.00 0.00 2.17
2490 2776 9.044150 TGTTCATGGATTCAAGAAAATTGTTTC 57.956 29.630 0.00 0.00 43.05 2.78
2581 2867 3.007940 GGGCCCTTTTGCTAGAACAAAAT 59.992 43.478 17.04 0.00 45.66 1.82
2627 2915 8.562892 GTGATCATGTCCATTGGAGTTTATAAG 58.437 37.037 5.39 0.00 29.39 1.73
2634 2923 4.515028 ATGTGATCATGTCCATTGGAGT 57.485 40.909 5.39 0.00 32.51 3.85
2801 3090 6.925610 TCCATGATCTTAGAAAATGTTCGG 57.074 37.500 0.00 0.00 38.90 4.30
2868 3160 8.898761 TGTTGCTCTAGTCAAGAAAAACATTTA 58.101 29.630 0.00 0.00 35.89 1.40
2884 3176 5.968848 GTCGATTCTAGAAGTGTTGCTCTAG 59.031 44.000 11.53 0.56 34.94 2.43
2889 3181 3.499048 TCGTCGATTCTAGAAGTGTTGC 58.501 45.455 11.53 0.00 0.00 4.17
2890 3182 4.915667 TGTTCGTCGATTCTAGAAGTGTTG 59.084 41.667 11.53 0.00 0.00 3.33
2895 3187 7.475565 CACAAAAATGTTCGTCGATTCTAGAAG 59.524 37.037 11.53 0.00 0.00 2.85
2919 3211 4.130286 TGTTCCACCAAACAATTTCCAC 57.870 40.909 0.00 0.00 36.25 4.02
2975 3267 4.738124 TCACGCATTTCAAAAAGTGTTCA 58.262 34.783 0.00 0.00 29.08 3.18
2979 3271 6.456447 AATGATCACGCATTTCAAAAAGTG 57.544 33.333 0.00 0.00 35.01 3.16


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

AutoCloner maintained by Alex Coulton.