Multiple sequence alignment - TraesCS3A01G473200

Loading Multiple Alignment...

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 TraesCS3A01G473200 chr3A 100.000 1500 0 0 813 2312 704353449 704354948 0.000000e+00 2771
1 TraesCS3A01G473200 chr3A 100.000 420 0 0 1 420 704352637 704353056 0.000000e+00 776
2 TraesCS3A01G473200 chr3A 85.210 453 38 10 1803 2253 704458525 704458950 2.730000e-119 438
3 TraesCS3A01G473200 chr3A 92.000 225 13 1 2088 2312 704451393 704451612 6.200000e-81 311
4 TraesCS3A01G473200 chr3A 78.864 440 73 12 852 1290 399678509 399678089 1.750000e-71 279
5 TraesCS3A01G473200 chr3A 89.595 173 15 1 63 232 704456423 704456595 1.390000e-52 217
6 TraesCS3A01G473200 chr3A 100.000 40 0 0 320 359 704352917 704352956 8.860000e-10 75
7 TraesCS3A01G473200 chr3A 100.000 40 0 0 281 320 704352956 704352995 8.860000e-10 75
8 TraesCS3A01G473200 chr3B 91.837 1519 95 18 818 2312 759093201 759094714 0.000000e+00 2091
9 TraesCS3A01G473200 chr3B 85.432 556 67 9 1758 2309 758852128 758852673 1.200000e-157 566
10 TraesCS3A01G473200 chr3B 84.400 500 48 8 1758 2257 758828887 758829356 4.500000e-127 464
11 TraesCS3A01G473200 chr3B 92.857 322 20 2 1 320 759091371 759091691 4.500000e-127 464
12 TraesCS3A01G473200 chr3B 84.000 500 49 9 1758 2257 758748645 758749113 3.500000e-123 451
13 TraesCS3A01G473200 chr3B 84.726 419 42 11 1758 2172 759098968 759099368 1.290000e-107 399
14 TraesCS3A01G473200 chr3B 88.987 227 25 0 6 232 758851870 758852096 4.860000e-72 281
15 TraesCS3A01G473200 chr3B 78.125 448 76 10 1286 1712 395862934 395862488 4.900000e-67 265
16 TraesCS3A01G473200 chr3B 83.333 264 31 7 2050 2312 758642136 758642387 4.970000e-57 231
17 TraesCS3A01G473200 chr3B 90.977 133 12 0 2125 2257 758969192 758969324 1.830000e-41 180
18 TraesCS3A01G473200 chr3B 94.366 71 4 0 2229 2299 759099394 759099464 2.430000e-20 110
19 TraesCS3A01G473200 chr2D 82.241 473 66 7 818 1290 600136750 600136296 2.150000e-105 392
20 TraesCS3A01G473200 chr2D 82.437 279 48 1 1012 1290 469184579 469184856 2.300000e-60 243
21 TraesCS3A01G473200 chr2D 79.412 340 58 7 826 1164 83046108 83046436 1.790000e-56 230
22 TraesCS3A01G473200 chr2D 80.827 266 51 0 1025 1290 536391883 536391618 2.330000e-50 209
23 TraesCS3A01G473200 chr7D 83.412 422 60 4 869 1290 454069524 454069113 1.300000e-102 383
24 TraesCS3A01G473200 chr7D 81.410 468 68 10 824 1290 575755258 575754809 4.690000e-97 364
25 TraesCS3A01G473200 chr7B 81.741 471 53 15 818 1288 337157665 337157228 1.690000e-96 363
26 TraesCS3A01G473200 chr5B 81.441 458 62 11 834 1290 514072112 514072547 1.020000e-93 353
27 TraesCS3A01G473200 chr5B 79.079 478 86 11 816 1290 290132485 290132019 1.330000e-82 316
28 TraesCS3A01G473200 chr5B 79.322 295 45 10 1421 1707 682120164 682119878 2.340000e-45 193
29 TraesCS3A01G473200 chr6B 80.258 466 77 11 818 1281 262277825 262278277 1.020000e-88 337
30 TraesCS3A01G473200 chr6A 79.536 474 66 8 818 1290 585085393 585085836 2.230000e-80 309
31 TraesCS3A01G473200 chr4A 79.337 392 64 9 1282 1658 519176450 519176839 2.280000e-65 259
32 TraesCS3A01G473200 chr2B 78.112 466 63 23 1282 1714 549676515 549676974 2.280000e-65 259
33 TraesCS3A01G473200 chr6D 77.143 455 74 15 1282 1708 405659698 405660150 1.070000e-58 237
34 TraesCS3A01G473200 chr1A 76.433 471 81 15 820 1290 547421439 547421879 6.430000e-56 228
35 TraesCS3A01G473200 chr1A 82.645 242 37 2 1421 1662 486895508 486895744 2.330000e-50 209
36 TraesCS3A01G473200 chr5D 77.670 412 65 8 1282 1666 305894500 305894089 2.310000e-55 226
37 TraesCS3A01G473200 chr3D 85.542 166 19 2 1758 1922 571853392 571853553 3.950000e-38 169


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 TraesCS3A01G473200 chr3A 704352637 704354948 2311 False 924.25 2771 100.0000 1 2312 4 chr3A.!!$F2 2311
1 TraesCS3A01G473200 chr3A 704456423 704458950 2527 False 327.50 438 87.4025 63 2253 2 chr3A.!!$F3 2190
2 TraesCS3A01G473200 chr3B 759091371 759094714 3343 False 1277.50 2091 92.3470 1 2312 2 chr3B.!!$F6 2311
3 TraesCS3A01G473200 chr3B 758851870 758852673 803 False 423.50 566 87.2095 6 2309 2 chr3B.!!$F5 2303

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
339 345 0.033781 CAGGTTGTCCGGACCGTAAA 59.966 55.0 31.19 16.24 42.11 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1703 2760 0.108615 ATCTTCCGTTCCGCAGACAG 60.109 55.0 0.0 0.0 0.0 3.51 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
29 30 4.720649 ACTATCTCGTTTGCTAGCTGAA 57.279 40.909 17.23 8.11 0.00 3.02
144 150 2.572191 TTACCGCTTCGATGGTACTG 57.428 50.000 10.29 0.00 40.34 2.74
272 278 0.958876 CCAGTAAACCTCCCGCAACC 60.959 60.000 0.00 0.00 0.00 3.77
276 282 0.603439 TAAACCTCCCGCAACCGTTC 60.603 55.000 0.00 0.00 0.00 3.95
277 283 4.675029 ACCTCCCGCAACCGTTCG 62.675 66.667 0.00 0.00 0.00 3.95
298 304 0.612732 ATCAGGTTGTCCGGACCGTA 60.613 55.000 31.19 14.21 40.41 4.02
303 309 1.733912 GGTTGTCCGGACCGTAAAATC 59.266 52.381 31.19 15.13 0.00 2.17
304 310 1.733912 GTTGTCCGGACCGTAAAATCC 59.266 52.381 31.19 3.08 0.00 3.01
305 311 0.975135 TGTCCGGACCGTAAAATCCA 59.025 50.000 31.19 6.03 34.35 3.41
306 312 1.555992 TGTCCGGACCGTAAAATCCAT 59.444 47.619 31.19 0.00 34.35 3.41
307 313 2.207590 GTCCGGACCGTAAAATCCATC 58.792 52.381 24.75 0.00 34.35 3.51
308 314 2.112998 TCCGGACCGTAAAATCCATCT 58.887 47.619 13.94 0.00 34.35 2.90
309 315 3.068590 GTCCGGACCGTAAAATCCATCTA 59.931 47.826 24.75 0.00 34.35 1.98
310 316 3.705579 TCCGGACCGTAAAATCCATCTAA 59.294 43.478 13.94 0.00 34.35 2.10
311 317 4.056050 CCGGACCGTAAAATCCATCTAAG 58.944 47.826 13.94 0.00 34.35 2.18
312 318 4.056050 CGGACCGTAAAATCCATCTAAGG 58.944 47.826 5.48 0.00 34.35 2.69
313 319 3.813724 GGACCGTAAAATCCATCTAAGGC 59.186 47.826 0.00 0.00 34.87 4.35
314 320 4.444449 GGACCGTAAAATCCATCTAAGGCT 60.444 45.833 0.00 0.00 34.87 4.58
315 321 4.451900 ACCGTAAAATCCATCTAAGGCTG 58.548 43.478 0.00 0.00 0.00 4.85
316 322 4.163458 ACCGTAAAATCCATCTAAGGCTGA 59.837 41.667 0.00 0.00 0.00 4.26
317 323 4.511826 CCGTAAAATCCATCTAAGGCTGAC 59.488 45.833 0.00 0.00 0.00 3.51
318 324 5.360591 CGTAAAATCCATCTAAGGCTGACT 58.639 41.667 0.00 0.00 0.00 3.41
319 325 5.817816 CGTAAAATCCATCTAAGGCTGACTT 59.182 40.000 0.00 0.00 43.28 3.01
320 326 6.018669 CGTAAAATCCATCTAAGGCTGACTTC 60.019 42.308 0.00 0.00 40.64 3.01
321 327 5.441718 AAATCCATCTAAGGCTGACTTCA 57.558 39.130 0.00 0.00 40.64 3.02
322 328 4.686191 ATCCATCTAAGGCTGACTTCAG 57.314 45.455 0.00 1.56 46.40 3.02
323 329 2.768527 TCCATCTAAGGCTGACTTCAGG 59.231 50.000 0.00 0.00 43.94 3.86
324 330 2.503356 CCATCTAAGGCTGACTTCAGGT 59.497 50.000 0.00 0.00 43.94 4.00
325 331 3.054802 CCATCTAAGGCTGACTTCAGGTT 60.055 47.826 0.00 0.00 43.94 3.50
326 332 3.685139 TCTAAGGCTGACTTCAGGTTG 57.315 47.619 0.00 0.00 43.94 3.77
327 333 2.972713 TCTAAGGCTGACTTCAGGTTGT 59.027 45.455 0.00 0.00 43.94 3.32
328 334 2.262423 AAGGCTGACTTCAGGTTGTC 57.738 50.000 8.32 0.00 43.94 3.18
329 335 0.398318 AGGCTGACTTCAGGTTGTCC 59.602 55.000 8.32 0.67 43.94 4.02
330 336 0.951040 GGCTGACTTCAGGTTGTCCG 60.951 60.000 8.32 0.00 43.94 4.79
331 337 0.951040 GCTGACTTCAGGTTGTCCGG 60.951 60.000 8.32 0.00 43.94 5.14
332 338 0.679505 CTGACTTCAGGTTGTCCGGA 59.320 55.000 0.00 0.00 40.20 5.14
333 339 0.391597 TGACTTCAGGTTGTCCGGAC 59.608 55.000 28.17 28.17 37.63 4.79
334 340 0.320508 GACTTCAGGTTGTCCGGACC 60.321 60.000 31.19 17.45 37.63 4.46
335 341 1.374252 CTTCAGGTTGTCCGGACCG 60.374 63.158 31.19 14.39 42.11 4.79
336 342 2.095978 CTTCAGGTTGTCCGGACCGT 62.096 60.000 31.19 15.56 42.11 4.83
337 343 0.827089 TTCAGGTTGTCCGGACCGTA 60.827 55.000 31.19 14.21 42.11 4.02
338 344 0.827089 TCAGGTTGTCCGGACCGTAA 60.827 55.000 31.19 16.62 42.11 3.18
339 345 0.033781 CAGGTTGTCCGGACCGTAAA 59.966 55.000 31.19 16.24 42.11 2.01
340 346 0.758123 AGGTTGTCCGGACCGTAAAA 59.242 50.000 31.19 15.85 42.11 1.52
341 347 1.348696 AGGTTGTCCGGACCGTAAAAT 59.651 47.619 31.19 8.59 42.11 1.82
342 348 1.733912 GGTTGTCCGGACCGTAAAATC 59.266 52.381 31.19 15.13 0.00 2.17
343 349 1.733912 GTTGTCCGGACCGTAAAATCC 59.266 52.381 31.19 3.08 0.00 3.01
353 359 4.444449 GGACCGTAAAATCCATCTAAGGCT 60.444 45.833 0.00 0.00 34.87 4.58
365 371 4.302455 CATCTAAGGCTGACTTGTATCGG 58.698 47.826 5.89 0.00 40.37 4.18
375 381 0.815734 CTTGTATCGGTCCGTGGAGT 59.184 55.000 11.88 0.00 0.00 3.85
395 401 1.339342 TGGTACGGACGTGATCTCTCA 60.339 52.381 7.73 0.00 0.00 3.27
834 1891 2.368875 GTCTCCTGGACCACTCAAAAGA 59.631 50.000 0.00 0.00 38.93 2.52
840 1897 1.248486 GACCACTCAAAAGAAGGGCC 58.752 55.000 0.00 0.00 0.00 5.80
922 1979 4.421479 CTTCACGCCGCTCTCCGT 62.421 66.667 0.00 0.00 38.35 4.69
930 1987 1.517832 CCGCTCTCCGTCCAATTCT 59.482 57.895 0.00 0.00 34.38 2.40
957 2014 0.252742 TTCTCCCACCCTCTCCTTCC 60.253 60.000 0.00 0.00 0.00 3.46
962 2019 1.081092 CACCCTCTCCTTCCCTCCA 59.919 63.158 0.00 0.00 0.00 3.86
963 2020 1.081277 ACCCTCTCCTTCCCTCCAC 59.919 63.158 0.00 0.00 0.00 4.02
974 2031 4.457496 CCTCCACTGCCGACGCAT 62.457 66.667 0.00 0.00 46.11 4.73
983 2040 1.808390 GCCGACGCATAGAACCGTT 60.808 57.895 0.00 0.00 37.87 4.44
985 2042 1.995991 CGACGCATAGAACCGTTGG 59.004 57.895 0.00 0.00 37.87 3.77
987 2044 0.997196 GACGCATAGAACCGTTGGAC 59.003 55.000 0.00 0.00 37.87 4.02
1067 2124 1.677217 GCTTGTCCGGAAGATCAGCTT 60.677 52.381 5.23 0.00 40.25 3.74
1068 2125 2.005451 CTTGTCCGGAAGATCAGCTTG 58.995 52.381 5.23 0.00 36.83 4.01
1079 2136 1.830587 ATCAGCTTGGAGACGTGGCA 61.831 55.000 0.00 0.00 0.00 4.92
1098 2155 1.469703 CAGAATCGCCATGTCAAAGCA 59.530 47.619 0.00 0.00 0.00 3.91
1100 2157 2.557924 AGAATCGCCATGTCAAAGCAAA 59.442 40.909 0.00 0.00 0.00 3.68
1103 2160 0.388907 CGCCATGTCAAAGCAAAGGG 60.389 55.000 0.00 0.00 0.00 3.95
1189 2246 3.311110 GACGAGGTGGACTGGGCA 61.311 66.667 0.00 0.00 32.32 5.36
1367 2424 7.461546 CGCTAGAATTATCATACAATCCGTTCG 60.462 40.741 0.00 0.00 0.00 3.95
1384 2441 2.515926 TCGCTATCAGATGTTGGAGC 57.484 50.000 0.00 0.00 34.62 4.70
1430 2487 1.982395 AAGATGAGGACGCGGTGGA 60.982 57.895 12.47 0.00 0.00 4.02
1441 2498 4.508128 CGGTGGATGCCTACGCGT 62.508 66.667 19.17 19.17 38.08 6.01
1469 2526 0.035439 GCACCTCCTTGATCGGGAAA 60.035 55.000 8.31 0.00 31.92 3.13
1496 2553 4.176752 GGGATGGCTGGTCCGGTC 62.177 72.222 0.00 0.00 36.58 4.79
1505 2562 4.011517 GGTCCGGTCGGGCAGAAA 62.012 66.667 16.07 0.00 42.75 2.52
1510 2567 2.877691 GGTCGGGCAGAAATGCAC 59.122 61.111 2.29 0.00 36.33 4.57
1530 2587 1.156736 GCACTGCCGTACTGATGTTT 58.843 50.000 0.00 0.00 0.00 2.83
1532 2589 2.739913 GCACTGCCGTACTGATGTTTTA 59.260 45.455 0.00 0.00 0.00 1.52
1540 2597 6.183360 TGCCGTACTGATGTTTTATTGGATTC 60.183 38.462 0.00 0.00 0.00 2.52
1609 2666 4.856801 GCGATCCGGCATGGGTGT 62.857 66.667 0.00 0.00 38.76 4.16
1610 2667 2.896854 CGATCCGGCATGGGTGTG 60.897 66.667 0.00 0.00 38.76 3.82
1625 2682 1.594862 GGTGTGATCTAGCGCATTGTC 59.405 52.381 11.47 2.78 0.00 3.18
1641 2698 4.697514 CATTGTCTGGGTCATCGTAGATT 58.302 43.478 0.00 0.00 45.12 2.40
1647 2704 5.817816 GTCTGGGTCATCGTAGATTTGAATT 59.182 40.000 0.00 0.00 45.12 2.17
1650 2707 6.176896 TGGGTCATCGTAGATTTGAATTTGA 58.823 36.000 0.00 0.00 45.12 2.69
1687 2744 3.430862 GCGGCTTGCGTTGGATGA 61.431 61.111 0.00 0.00 0.00 2.92
1688 2745 2.480555 CGGCTTGCGTTGGATGAC 59.519 61.111 0.00 0.00 0.00 3.06
1694 2751 0.955428 TTGCGTTGGATGACTGCCTC 60.955 55.000 0.00 0.00 0.00 4.70
1695 2752 2.109126 GCGTTGGATGACTGCCTCC 61.109 63.158 0.00 0.00 0.00 4.30
1697 2754 1.450312 GTTGGATGACTGCCTCCCG 60.450 63.158 0.00 0.00 0.00 5.14
1750 2828 0.180406 AGGTTGCTATGCCCTAACGG 59.820 55.000 0.00 0.00 0.00 4.44
1764 2842 0.901827 TAACGGCAGGAAGAGCATCA 59.098 50.000 0.00 0.00 37.82 3.07
1786 2864 3.083997 GCTGGGATCCGTGGGTCT 61.084 66.667 5.45 0.00 0.00 3.85
1787 2865 2.670148 GCTGGGATCCGTGGGTCTT 61.670 63.158 5.45 0.00 0.00 3.01
1788 2866 1.335132 GCTGGGATCCGTGGGTCTTA 61.335 60.000 5.45 0.00 0.00 2.10
1789 2867 1.200519 CTGGGATCCGTGGGTCTTAA 58.799 55.000 5.45 0.00 0.00 1.85
1887 4822 6.708949 AGTGTTACCTTGGTAAATGTAGTGTG 59.291 38.462 13.17 0.00 0.00 3.82
1904 4860 6.978659 TGTAGTGTGAAGATAATTTAGCGAGG 59.021 38.462 0.00 0.00 0.00 4.63
1907 4863 6.313905 AGTGTGAAGATAATTTAGCGAGGTTG 59.686 38.462 0.00 0.00 0.00 3.77
1969 4925 0.445043 GTTAGTTTTAGCACGCGGGG 59.555 55.000 11.92 2.33 0.00 5.73
1984 4940 1.690352 GCGGGGGTAAGTTCAGCTATA 59.310 52.381 0.00 0.00 0.00 1.31
2002 4958 6.094186 CAGCTATATATGCGTCCTCTAGACAA 59.906 42.308 0.00 0.00 46.69 3.18
2014 4970 5.989777 GTCCTCTAGACAAAACACAAAGCTA 59.010 40.000 0.00 0.00 45.55 3.32
2029 4985 0.537188 AGCTAAGTGACCACCCATCG 59.463 55.000 0.00 0.00 0.00 3.84
2041 4997 1.694150 CACCCATCGACCCATCTGTAT 59.306 52.381 0.00 0.00 0.00 2.29
2077 5033 7.472543 CCAGGAGTAAATCAAGAAATTAACCG 58.527 38.462 0.00 0.00 0.00 4.44
2109 5065 3.407424 TCATCCGATGCATTAGGGAAG 57.593 47.619 18.35 13.97 31.24 3.46
2116 5072 6.173339 TCCGATGCATTAGGGAAGAATAATC 58.827 40.000 18.35 0.00 0.00 1.75
2148 5104 1.523154 GCTGCCGGTTGTTTGGATGA 61.523 55.000 1.90 0.00 0.00 2.92
2152 5110 1.335872 GCCGGTTGTTTGGATGAACTG 60.336 52.381 1.90 0.00 0.00 3.16
2175 5133 0.392193 GCTACCAGCAGAGCATGTGT 60.392 55.000 0.00 0.00 41.89 3.72
2194 5152 4.460731 TGTGTGTGTTTGTCCTTTTCATCA 59.539 37.500 0.00 0.00 0.00 3.07
2215 5173 5.003160 TCAAGAAGATTCGCCTGATTTTGA 58.997 37.500 0.00 0.00 0.00 2.69
2221 5179 0.237235 TCGCCTGATTTTGAACGTGC 59.763 50.000 0.00 0.00 0.00 5.34
2238 5196 0.823356 TGCTGCGGGAAGAAAAGCTT 60.823 50.000 0.00 0.00 40.25 3.74
2284 5242 2.587889 GCCCGCTTAGGTAGGCAA 59.412 61.111 2.96 0.00 45.07 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.457148 CAGCTAGCAAACGAGATAGTACAAG 59.543 44.000 18.83 0.00 30.45 3.16
29 30 0.534877 TGTGAACATGCACGAAGGCT 60.535 50.000 0.00 0.00 41.63 4.58
144 150 1.356527 CGGCGGTACAAACTGGTAGC 61.357 60.000 0.00 0.00 38.15 3.58
194 200 0.676782 GCGATGGTGGCCAACTAACT 60.677 55.000 24.13 3.66 36.95 2.24
246 252 2.047560 AGGTTTACTGGTCGGCGC 60.048 61.111 0.00 0.00 0.00 6.53
248 254 1.078637 GGGAGGTTTACTGGTCGGC 60.079 63.158 0.00 0.00 0.00 5.54
272 278 2.750815 GGACAACCTGATCCGAACG 58.249 57.895 0.00 0.00 0.00 3.95
277 283 1.221021 GGTCCGGACAACCTGATCC 59.779 63.158 34.40 11.59 32.42 3.36
282 288 0.758123 TTTTACGGTCCGGACAACCT 59.242 50.000 34.40 16.00 34.45 3.50
298 304 5.819991 TGAAGTCAGCCTTAGATGGATTTT 58.180 37.500 0.00 0.00 32.03 1.82
303 309 2.503356 ACCTGAAGTCAGCCTTAGATGG 59.497 50.000 2.59 0.00 42.47 3.51
304 310 3.902881 ACCTGAAGTCAGCCTTAGATG 57.097 47.619 2.59 0.00 42.47 2.90
305 311 3.584848 ACAACCTGAAGTCAGCCTTAGAT 59.415 43.478 2.59 0.00 42.47 1.98
306 312 2.972713 ACAACCTGAAGTCAGCCTTAGA 59.027 45.455 2.59 0.00 42.47 2.10
307 313 3.330267 GACAACCTGAAGTCAGCCTTAG 58.670 50.000 2.59 0.00 42.47 2.18
308 314 2.038557 GGACAACCTGAAGTCAGCCTTA 59.961 50.000 2.59 0.00 42.47 2.69
309 315 1.202818 GGACAACCTGAAGTCAGCCTT 60.203 52.381 2.59 0.00 42.47 4.35
310 316 0.398318 GGACAACCTGAAGTCAGCCT 59.602 55.000 2.59 0.00 42.47 4.58
311 317 0.951040 CGGACAACCTGAAGTCAGCC 60.951 60.000 2.59 0.00 42.47 4.85
312 318 0.951040 CCGGACAACCTGAAGTCAGC 60.951 60.000 0.00 0.00 42.47 4.26
313 319 0.679505 TCCGGACAACCTGAAGTCAG 59.320 55.000 0.00 1.05 43.40 3.51
314 320 0.391597 GTCCGGACAACCTGAAGTCA 59.608 55.000 29.75 0.00 36.50 3.41
315 321 0.320508 GGTCCGGACAACCTGAAGTC 60.321 60.000 34.40 10.52 33.78 3.01
316 322 1.752833 GGTCCGGACAACCTGAAGT 59.247 57.895 34.40 0.00 33.78 3.01
317 323 1.374252 CGGTCCGGACAACCTGAAG 60.374 63.158 34.40 11.64 34.45 3.02
318 324 0.827089 TACGGTCCGGACAACCTGAA 60.827 55.000 34.40 10.53 34.45 3.02
319 325 0.827089 TTACGGTCCGGACAACCTGA 60.827 55.000 34.40 13.04 34.45 3.86
320 326 0.033781 TTTACGGTCCGGACAACCTG 59.966 55.000 34.40 19.96 34.45 4.00
321 327 0.758123 TTTTACGGTCCGGACAACCT 59.242 50.000 34.40 16.00 34.45 3.50
322 328 1.733912 GATTTTACGGTCCGGACAACC 59.266 52.381 34.40 18.46 0.00 3.77
323 329 1.733912 GGATTTTACGGTCCGGACAAC 59.266 52.381 34.40 18.08 0.00 3.32
324 330 1.347050 TGGATTTTACGGTCCGGACAA 59.653 47.619 34.40 20.54 37.32 3.18
325 331 0.975135 TGGATTTTACGGTCCGGACA 59.025 50.000 34.40 14.72 37.32 4.02
326 332 2.159000 AGATGGATTTTACGGTCCGGAC 60.159 50.000 27.04 27.04 37.32 4.79
327 333 2.112998 AGATGGATTTTACGGTCCGGA 58.887 47.619 17.28 3.30 37.32 5.14
328 334 2.614829 AGATGGATTTTACGGTCCGG 57.385 50.000 17.28 0.00 37.32 5.14
329 335 4.056050 CCTTAGATGGATTTTACGGTCCG 58.944 47.826 10.48 10.48 37.32 4.79
330 336 3.813724 GCCTTAGATGGATTTTACGGTCC 59.186 47.826 0.00 0.00 35.02 4.46
331 337 4.511826 CAGCCTTAGATGGATTTTACGGTC 59.488 45.833 0.00 0.00 0.00 4.79
332 338 4.163458 TCAGCCTTAGATGGATTTTACGGT 59.837 41.667 0.00 0.00 0.00 4.83
333 339 4.511826 GTCAGCCTTAGATGGATTTTACGG 59.488 45.833 0.00 0.00 0.00 4.02
334 340 5.360591 AGTCAGCCTTAGATGGATTTTACG 58.639 41.667 0.00 0.00 0.00 3.18
335 341 6.599638 ACAAGTCAGCCTTAGATGGATTTTAC 59.400 38.462 0.00 0.00 0.00 2.01
336 342 6.721318 ACAAGTCAGCCTTAGATGGATTTTA 58.279 36.000 0.00 0.00 0.00 1.52
337 343 5.574188 ACAAGTCAGCCTTAGATGGATTTT 58.426 37.500 0.00 0.00 0.00 1.82
338 344 5.184892 ACAAGTCAGCCTTAGATGGATTT 57.815 39.130 0.00 0.00 0.00 2.17
339 345 4.851639 ACAAGTCAGCCTTAGATGGATT 57.148 40.909 0.00 0.00 0.00 3.01
340 346 5.279206 CGATACAAGTCAGCCTTAGATGGAT 60.279 44.000 0.00 0.00 0.00 3.41
341 347 4.038042 CGATACAAGTCAGCCTTAGATGGA 59.962 45.833 0.00 0.00 0.00 3.41
342 348 4.302455 CGATACAAGTCAGCCTTAGATGG 58.698 47.826 0.00 0.00 0.00 3.51
343 349 4.202161 ACCGATACAAGTCAGCCTTAGATG 60.202 45.833 0.00 0.00 0.00 2.90
353 359 0.528924 CCACGGACCGATACAAGTCA 59.471 55.000 23.38 0.00 34.58 3.41
375 381 1.339342 TGAGAGATCACGTCCGTACCA 60.339 52.381 0.00 0.00 0.00 3.25
395 401 3.938963 ACATGTTTATCTCCGATTTGCGT 59.061 39.130 0.00 0.00 38.67 5.24
812 818 2.103153 TTTGAGTGGTCCAGGAGACT 57.897 50.000 0.00 1.10 45.54 3.24
814 820 2.689658 TCTTTTGAGTGGTCCAGGAGA 58.310 47.619 0.00 0.00 0.00 3.71
815 821 3.406764 CTTCTTTTGAGTGGTCCAGGAG 58.593 50.000 0.00 0.00 0.00 3.69
816 822 2.106511 CCTTCTTTTGAGTGGTCCAGGA 59.893 50.000 0.00 0.00 0.00 3.86
818 824 2.508526 CCCTTCTTTTGAGTGGTCCAG 58.491 52.381 0.00 0.00 0.00 3.86
819 825 1.478654 GCCCTTCTTTTGAGTGGTCCA 60.479 52.381 0.00 0.00 0.00 4.02
820 826 1.248486 GCCCTTCTTTTGAGTGGTCC 58.752 55.000 0.00 0.00 0.00 4.46
821 827 1.248486 GGCCCTTCTTTTGAGTGGTC 58.752 55.000 0.00 0.00 0.00 4.02
822 828 0.537371 CGGCCCTTCTTTTGAGTGGT 60.537 55.000 0.00 0.00 0.00 4.16
823 829 0.250727 TCGGCCCTTCTTTTGAGTGG 60.251 55.000 0.00 0.00 0.00 4.00
862 1919 2.502510 GCGCGGAAACAGTGCATG 60.503 61.111 8.83 0.00 43.84 4.06
922 1979 4.080582 TGGGAGAAAATAGCGAGAATTGGA 60.081 41.667 0.00 0.00 0.00 3.53
930 1987 1.485066 GAGGGTGGGAGAAAATAGCGA 59.515 52.381 0.00 0.00 0.00 4.93
974 2031 3.460103 GACAAGTTGTCCAACGGTTCTA 58.540 45.455 23.03 0.00 45.50 2.10
983 2040 1.001974 CCATCTCCGACAAGTTGTCCA 59.998 52.381 26.37 14.49 44.20 4.02
985 2042 2.611518 CTCCATCTCCGACAAGTTGTC 58.388 52.381 23.53 23.53 43.65 3.18
987 2044 2.009042 GCCTCCATCTCCGACAAGTTG 61.009 57.143 0.00 0.00 0.00 3.16
1046 2103 1.424493 GCTGATCTTCCGGACAAGCG 61.424 60.000 1.83 0.00 0.00 4.68
1067 2124 1.215382 CGATTCTGCCACGTCTCCA 59.785 57.895 0.00 0.00 0.00 3.86
1068 2125 2.167861 GCGATTCTGCCACGTCTCC 61.168 63.158 0.00 0.00 0.00 3.71
1079 2136 1.825090 TGCTTTGACATGGCGATTCT 58.175 45.000 0.00 0.00 0.00 2.40
1089 2146 1.670949 TTGCGCCCTTTGCTTTGACA 61.671 50.000 4.18 0.00 38.05 3.58
1098 2155 1.303643 CTCCTCCTTTGCGCCCTTT 60.304 57.895 4.18 0.00 0.00 3.11
1100 2157 2.190488 CTTCTCCTCCTTTGCGCCCT 62.190 60.000 4.18 0.00 0.00 5.19
1103 2160 1.012841 CATCTTCTCCTCCTTTGCGC 58.987 55.000 0.00 0.00 0.00 6.09
1266 2323 2.159462 GGCGGCGTAGTAGTATGGATAC 60.159 54.545 9.37 0.00 0.00 2.24
1268 2325 0.886563 GGCGGCGTAGTAGTATGGAT 59.113 55.000 9.37 0.00 0.00 3.41
1298 2355 1.202758 TCAAGGTTCACATCTTGGCGT 60.203 47.619 0.00 0.00 40.35 5.68
1367 2424 1.506493 CCGCTCCAACATCTGATAGC 58.494 55.000 0.00 0.00 33.07 2.97
1384 2441 0.449388 GCCAACTGATCTTTCTGCCG 59.551 55.000 0.00 0.00 0.00 5.69
1469 2526 0.395311 CAGCCATCCCAGCAAGATGT 60.395 55.000 9.06 0.00 39.62 3.06
1510 2567 1.014044 AACATCAGTACGGCAGTGCG 61.014 55.000 9.45 7.22 38.06 5.34
1530 2587 6.153680 ACTTTTTACATGCCCGAATCCAATAA 59.846 34.615 0.00 0.00 0.00 1.40
1532 2589 4.466015 ACTTTTTACATGCCCGAATCCAAT 59.534 37.500 0.00 0.00 0.00 3.16
1540 2597 9.445786 CAAATATACTTACTTTTTACATGCCCG 57.554 33.333 0.00 0.00 0.00 6.13
1602 2659 0.761187 ATGCGCTAGATCACACCCAT 59.239 50.000 9.73 0.00 0.00 4.00
1609 2666 1.202568 CCCAGACAATGCGCTAGATCA 60.203 52.381 9.73 0.00 0.00 2.92
1610 2667 1.202580 ACCCAGACAATGCGCTAGATC 60.203 52.381 9.73 1.17 0.00 2.75
1625 2682 6.316140 TCAAATTCAAATCTACGATGACCCAG 59.684 38.462 0.00 0.00 0.00 4.45
1647 2704 7.413988 CCGCATATTGTCTGTCAGTAAATTCAA 60.414 37.037 0.00 0.00 0.00 2.69
1650 2707 5.220854 GCCGCATATTGTCTGTCAGTAAATT 60.221 40.000 0.00 0.00 0.00 1.82
1655 2712 1.208052 AGCCGCATATTGTCTGTCAGT 59.792 47.619 0.00 0.00 0.00 3.41
1658 2715 1.268234 GCAAGCCGCATATTGTCTGTC 60.268 52.381 0.00 0.00 41.79 3.51
1697 2754 2.109126 GTTCCGCAGACAGGGATGC 61.109 63.158 0.00 0.00 39.09 3.91
1701 2758 3.234630 TTCCGTTCCGCAGACAGGG 62.235 63.158 0.00 0.00 0.00 4.45
1703 2760 0.108615 ATCTTCCGTTCCGCAGACAG 60.109 55.000 0.00 0.00 0.00 3.51
1730 2808 1.299541 CGTTAGGGCATAGCAACCTG 58.700 55.000 0.00 0.00 35.84 4.00
1750 2828 0.809241 CTCGGTGATGCTCTTCCTGC 60.809 60.000 0.00 0.00 0.00 4.85
1764 2842 3.461773 CACGGATCCCAGCTCGGT 61.462 66.667 6.06 0.00 0.00 4.69
1887 4822 4.318831 CCGCAACCTCGCTAAATTATCTTC 60.319 45.833 0.00 0.00 0.00 2.87
1904 4860 4.742438 TCTCACTAAATTTCACCGCAAC 57.258 40.909 0.00 0.00 0.00 4.17
1907 4863 3.938963 TGGATCTCACTAAATTTCACCGC 59.061 43.478 0.00 0.00 0.00 5.68
1961 4917 1.740296 CTGAACTTACCCCCGCGTG 60.740 63.158 4.92 0.00 0.00 5.34
1969 4925 5.805994 GGACGCATATATAGCTGAACTTACC 59.194 44.000 0.00 0.00 0.00 2.85
2002 4958 3.380320 GGTGGTCACTTAGCTTTGTGTTT 59.620 43.478 15.31 0.00 35.82 2.83
2014 4970 1.677552 GGTCGATGGGTGGTCACTT 59.322 57.895 0.93 0.00 0.00 3.16
2029 4985 4.740934 GCAACCTACTCATACAGATGGGTC 60.741 50.000 0.00 0.00 43.82 4.46
2041 4997 2.615986 TACTCCTGGCAACCTACTCA 57.384 50.000 0.00 0.00 0.00 3.41
2077 5033 0.251916 TCGGATGAATCACCACCACC 59.748 55.000 0.00 0.00 0.00 4.61
2109 5065 7.113965 CGGCAGCAAACATAATCTTGATTATTC 59.886 37.037 11.81 2.55 0.00 1.75
2116 5072 2.164219 ACCGGCAGCAAACATAATCTTG 59.836 45.455 0.00 0.00 0.00 3.02
2152 5110 1.694133 ATGCTCTGCTGGTAGCTCCC 61.694 60.000 0.00 0.00 42.97 4.30
2175 5133 6.376864 TCTTCTTGATGAAAAGGACAAACACA 59.623 34.615 0.00 0.00 33.79 3.72
2194 5152 5.617751 CGTTCAAAATCAGGCGAATCTTCTT 60.618 40.000 0.00 0.00 0.00 2.52
2215 5173 1.098712 TTTTCTTCCCGCAGCACGTT 61.099 50.000 0.00 0.00 41.42 3.99
2238 5196 1.559682 GCTCCTTAATCCACACTGGGA 59.440 52.381 0.00 0.00 42.21 4.37
2284 5242 1.078709 CAAGCACGTGAATGGTCGAT 58.921 50.000 22.23 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.