Multiple sequence alignment - TraesCS6A01G369100

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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 TraesCS6A01G369100 chr6A 100.000 3718 0 0 1 3718 594853296 594857013 0.000000e+00 6866
1 TraesCS6A01G369100 chr6A 93.606 2862 114 24 904 3718 594938760 594941599 0.000000e+00 4207
2 TraesCS6A01G369100 chr6A 82.713 1961 211 63 1480 3394 594948922 594950800 0.000000e+00 1626
3 TraesCS6A01G369100 chr6A 82.178 707 84 24 14 695 511036586 511035897 1.500000e-158 569
4 TraesCS6A01G369100 chr6A 82.864 391 55 9 308 690 523070200 523070586 1.280000e-89 340
5 TraesCS6A01G369100 chr6A 85.149 303 34 9 933 1230 594948603 594948899 2.170000e-77 300
6 TraesCS6A01G369100 chr6A 79.167 432 63 15 2398 2816 594965930 594966347 1.320000e-69 274
7 TraesCS6A01G369100 chr6A 85.366 246 30 3 14 256 498956254 498956012 2.220000e-62 250
8 TraesCS6A01G369100 chr6A 78.655 342 58 9 2398 2729 595065777 595065441 2.910000e-51 213
9 TraesCS6A01G369100 chr6A 75.878 427 90 9 2398 2816 595163522 595163943 4.870000e-49 206
10 TraesCS6A01G369100 chr6A 76.640 381 66 16 1396 1768 24285155 24285520 4.900000e-44 189
11 TraesCS6A01G369100 chr6D 90.372 2877 194 34 888 3718 448803860 448806699 0.000000e+00 3701
12 TraesCS6A01G369100 chr6D 89.595 1903 158 15 697 2584 448798936 448800813 0.000000e+00 2381
13 TraesCS6A01G369100 chr6D 84.825 916 98 22 2820 3718 448801153 448802044 0.000000e+00 883
14 TraesCS6A01G369100 chr6D 78.009 1487 242 40 1397 2817 448818102 448819569 0.000000e+00 856
15 TraesCS6A01G369100 chr6D 78.074 675 114 22 1159 1828 448842841 448843486 2.690000e-106 396
16 TraesCS6A01G369100 chr6D 92.276 246 14 2 2574 2815 448800839 448801083 9.890000e-91 344
17 TraesCS6A01G369100 chr6D 80.687 466 70 14 2365 2816 448843792 448844251 9.890000e-91 344
18 TraesCS6A01G369100 chr6D 73.913 874 196 23 1094 1960 449775966 449776814 4.630000e-84 322
19 TraesCS6A01G369100 chr6D 88.333 240 25 1 14 253 356288380 356288144 6.080000e-73 285
20 TraesCS6A01G369100 chr6B 95.327 1391 35 7 1845 3217 680530807 680529429 0.000000e+00 2182
21 TraesCS6A01G369100 chr6B 82.642 1953 270 45 888 2816 680701180 680703087 0.000000e+00 1664
22 TraesCS6A01G369100 chr6B 89.132 1187 71 24 696 1857 680532130 680530977 0.000000e+00 1424
23 TraesCS6A01G369100 chr6B 93.256 519 21 4 3200 3718 680529246 680528742 0.000000e+00 752
24 TraesCS6A01G369100 chr6B 82.270 705 97 23 1 695 555338933 555338247 5.350000e-163 584
25 TraesCS6A01G369100 chr6B 76.442 416 73 14 2406 2816 681377407 681377802 6.300000e-48 202
26 TraesCS6A01G369100 chr5D 83.478 690 90 14 14 693 556143737 556143062 4.080000e-174 621
27 TraesCS6A01G369100 chr5D 86.364 264 29 5 14 274 450784581 450784322 7.860000e-72 281
28 TraesCS6A01G369100 chr5D 82.156 269 37 7 14 273 311477486 311477220 1.740000e-53 220
29 TraesCS6A01G369100 chr4D 82.284 683 95 21 14 693 16747830 16747171 5.390000e-158 568
30 TraesCS6A01G369100 chr3B 79.792 673 101 26 14 662 105951577 105950916 1.220000e-124 457
31 TraesCS6A01G369100 chr4A 82.305 486 73 13 215 691 583807925 583808406 3.460000e-110 409
32 TraesCS6A01G369100 chr3A 78.702 493 83 17 218 695 21363781 21363296 3.610000e-80 309
33 TraesCS6A01G369100 chr2D 82.133 375 50 16 326 693 112089443 112089807 4.670000e-79 305
34 TraesCS6A01G369100 chr7B 81.122 392 63 10 308 695 497009709 497009325 1.680000e-78 303
35 TraesCS6A01G369100 chr7B 89.256 242 23 2 14 255 497009955 497009717 2.170000e-77 300
36 TraesCS6A01G369100 chr7B 84.528 265 29 9 14 273 164542908 164543165 6.160000e-63 252
37 TraesCS6A01G369100 chr2B 81.053 380 54 16 323 693 161991828 161992198 1.690000e-73 287
38 TraesCS6A01G369100 chrUn 76.658 377 69 13 1396 1768 93793180 93793541 1.360000e-44 191


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 TraesCS6A01G369100 chr6A 594853296 594857013 3717 False 6866.000000 6866 100.000000 1 3718 1 chr6A.!!$F3 3717
1 TraesCS6A01G369100 chr6A 594938760 594941599 2839 False 4207.000000 4207 93.606000 904 3718 1 chr6A.!!$F4 2814
2 TraesCS6A01G369100 chr6A 594948603 594950800 2197 False 963.000000 1626 83.931000 933 3394 2 chr6A.!!$F7 2461
3 TraesCS6A01G369100 chr6A 511035897 511036586 689 True 569.000000 569 82.178000 14 695 1 chr6A.!!$R2 681
4 TraesCS6A01G369100 chr6D 448798936 448806699 7763 False 1827.250000 3701 89.267000 697 3718 4 chr6D.!!$F3 3021
5 TraesCS6A01G369100 chr6D 448818102 448819569 1467 False 856.000000 856 78.009000 1397 2817 1 chr6D.!!$F1 1420
6 TraesCS6A01G369100 chr6D 448842841 448844251 1410 False 370.000000 396 79.380500 1159 2816 2 chr6D.!!$F4 1657
7 TraesCS6A01G369100 chr6D 449775966 449776814 848 False 322.000000 322 73.913000 1094 1960 1 chr6D.!!$F2 866
8 TraesCS6A01G369100 chr6B 680701180 680703087 1907 False 1664.000000 1664 82.642000 888 2816 1 chr6B.!!$F1 1928
9 TraesCS6A01G369100 chr6B 680528742 680532130 3388 True 1452.666667 2182 92.571667 696 3718 3 chr6B.!!$R2 3022
10 TraesCS6A01G369100 chr6B 555338247 555338933 686 True 584.000000 584 82.270000 1 695 1 chr6B.!!$R1 694
11 TraesCS6A01G369100 chr5D 556143062 556143737 675 True 621.000000 621 83.478000 14 693 1 chr5D.!!$R3 679
12 TraesCS6A01G369100 chr4D 16747171 16747830 659 True 568.000000 568 82.284000 14 693 1 chr4D.!!$R1 679
13 TraesCS6A01G369100 chr3B 105950916 105951577 661 True 457.000000 457 79.792000 14 662 1 chr3B.!!$R1 648
14 TraesCS6A01G369100 chr7B 497009325 497009955 630 True 301.500000 303 85.189000 14 695 2 chr7B.!!$R1 681

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
607 722 0.743688 ACCAAACAATGCGCAGTTGA 59.256 45.0 27.69 3.38 0.00 3.18 F
1302 1473 0.609681 AGTCGAGTTTCCCGAGCTCT 60.610 55.0 12.85 0.00 36.66 4.09 F
1564 1768 0.824759 GATCCTACACCTTGAGCGGT 59.175 55.0 0.00 0.00 37.93 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1503 1707 1.264288 GGCGCATCAAGTATTAGTGGC 59.736 52.381 10.83 0.0 0.00 5.01 R
2236 7379 2.711547 AGTAAGCAGGAAGTTTGGGACT 59.288 45.455 0.00 0.0 41.47 3.85 R
3497 8979 1.929836 GGCGAGCAGTTTGATGTAGAG 59.070 52.381 0.00 0.0 0.00 2.43 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
50 51 3.501445 GCATTCTGCATACTTGGATCCTC 59.499 47.826 14.23 0.00 44.26 3.71
75 76 1.895131 GGGGCATTGATGAACTTGTGT 59.105 47.619 0.00 0.00 0.00 3.72
115 116 2.168521 CGCCTAAGGATCTTGACCTTGA 59.831 50.000 9.13 0.00 45.74 3.02
183 184 1.089920 GCTGAAGTGGGCACATACAG 58.910 55.000 13.18 13.18 34.13 2.74
238 254 3.324556 AGAAGAAGAAGAGCAAGAGCAGT 59.675 43.478 0.00 0.00 45.49 4.40
260 344 1.268079 GCAGAAGAGGAAGCAACAACC 59.732 52.381 0.00 0.00 0.00 3.77
262 346 2.951642 CAGAAGAGGAAGCAACAACCAA 59.048 45.455 0.00 0.00 0.00 3.67
275 359 4.566759 GCAACAACCAAAGAAGAGGAAAAC 59.433 41.667 0.00 0.00 0.00 2.43
276 360 5.719173 CAACAACCAAAGAAGAGGAAAACA 58.281 37.500 0.00 0.00 0.00 2.83
278 362 6.353404 ACAACCAAAGAAGAGGAAAACAAA 57.647 33.333 0.00 0.00 0.00 2.83
279 363 6.163476 ACAACCAAAGAAGAGGAAAACAAAC 58.837 36.000 0.00 0.00 0.00 2.93
280 364 5.993748 ACCAAAGAAGAGGAAAACAAACA 57.006 34.783 0.00 0.00 0.00 2.83
281 365 5.965922 ACCAAAGAAGAGGAAAACAAACAG 58.034 37.500 0.00 0.00 0.00 3.16
282 366 5.105351 ACCAAAGAAGAGGAAAACAAACAGG 60.105 40.000 0.00 0.00 0.00 4.00
283 367 5.127031 CCAAAGAAGAGGAAAACAAACAGGA 59.873 40.000 0.00 0.00 0.00 3.86
284 368 6.350949 CCAAAGAAGAGGAAAACAAACAGGAA 60.351 38.462 0.00 0.00 0.00 3.36
285 369 5.836821 AGAAGAGGAAAACAAACAGGAAC 57.163 39.130 0.00 0.00 0.00 3.62
286 370 5.261216 AGAAGAGGAAAACAAACAGGAACA 58.739 37.500 0.00 0.00 0.00 3.18
287 371 5.714806 AGAAGAGGAAAACAAACAGGAACAA 59.285 36.000 0.00 0.00 0.00 2.83
288 372 5.993748 AGAGGAAAACAAACAGGAACAAA 57.006 34.783 0.00 0.00 0.00 2.83
289 373 6.353404 AGAGGAAAACAAACAGGAACAAAA 57.647 33.333 0.00 0.00 0.00 2.44
290 374 6.398095 AGAGGAAAACAAACAGGAACAAAAG 58.602 36.000 0.00 0.00 0.00 2.27
291 375 5.487433 AGGAAAACAAACAGGAACAAAAGG 58.513 37.500 0.00 0.00 0.00 3.11
292 376 5.247337 AGGAAAACAAACAGGAACAAAAGGA 59.753 36.000 0.00 0.00 0.00 3.36
293 377 5.935206 GGAAAACAAACAGGAACAAAAGGAA 59.065 36.000 0.00 0.00 0.00 3.36
294 378 6.128391 GGAAAACAAACAGGAACAAAAGGAAC 60.128 38.462 0.00 0.00 0.00 3.62
295 379 5.476091 AACAAACAGGAACAAAAGGAACA 57.524 34.783 0.00 0.00 0.00 3.18
296 380 5.476091 ACAAACAGGAACAAAAGGAACAA 57.524 34.783 0.00 0.00 0.00 2.83
297 381 5.234752 ACAAACAGGAACAAAAGGAACAAC 58.765 37.500 0.00 0.00 0.00 3.32
298 382 3.775661 ACAGGAACAAAAGGAACAACG 57.224 42.857 0.00 0.00 0.00 4.10
299 383 2.425668 ACAGGAACAAAAGGAACAACGG 59.574 45.455 0.00 0.00 0.00 4.44
300 384 2.685897 CAGGAACAAAAGGAACAACGGA 59.314 45.455 0.00 0.00 0.00 4.69
301 385 3.129638 CAGGAACAAAAGGAACAACGGAA 59.870 43.478 0.00 0.00 0.00 4.30
302 386 3.380320 AGGAACAAAAGGAACAACGGAAG 59.620 43.478 0.00 0.00 0.00 3.46
303 387 3.379057 GGAACAAAAGGAACAACGGAAGA 59.621 43.478 0.00 0.00 0.00 2.87
304 388 4.497507 GGAACAAAAGGAACAACGGAAGAG 60.498 45.833 0.00 0.00 0.00 2.85
305 389 2.949644 ACAAAAGGAACAACGGAAGAGG 59.050 45.455 0.00 0.00 0.00 3.69
306 390 2.949644 CAAAAGGAACAACGGAAGAGGT 59.050 45.455 0.00 0.00 0.00 3.85
317 409 5.070047 ACAACGGAAGAGGTAAGAGAAAGAA 59.930 40.000 0.00 0.00 0.00 2.52
335 427 7.237255 AGAAAGAAGAGGGATGATGAACTTTT 58.763 34.615 0.00 0.00 0.00 2.27
343 435 5.126061 AGGGATGATGAACTTTTTCCATTCG 59.874 40.000 0.00 0.00 0.00 3.34
452 566 3.695830 AATCGTGTGTGGTAAGGTCAT 57.304 42.857 0.00 0.00 0.00 3.06
467 581 6.071278 GGTAAGGTCATCACTAGTGAGAAGTT 60.071 42.308 28.29 20.63 43.61 2.66
474 588 4.933330 TCACTAGTGAGAAGTTGTGACAC 58.067 43.478 21.74 0.00 34.14 3.67
477 591 3.845781 AGTGAGAAGTTGTGACACCAT 57.154 42.857 2.45 0.00 32.76 3.55
514 628 5.113383 CAACCAAATAGCGTGTCCTATGTA 58.887 41.667 0.00 0.00 0.00 2.29
524 638 3.243301 CGTGTCCTATGTACGCCTAATGT 60.243 47.826 0.00 0.00 0.00 2.71
543 657 1.040646 TTATGCGGCCAACCAAACAA 58.959 45.000 2.24 0.00 34.57 2.83
551 666 1.915952 CCAACCAAACAACGGTCAAC 58.084 50.000 0.00 0.00 34.99 3.18
562 677 3.120041 CAACGGTCAACATTTGTTTCCC 58.880 45.455 0.00 0.00 35.83 3.97
566 681 5.562635 ACGGTCAACATTTGTTTCCCTATA 58.437 37.500 0.00 0.00 35.83 1.31
567 682 6.005198 ACGGTCAACATTTGTTTCCCTATAA 58.995 36.000 0.00 0.00 35.83 0.98
570 685 7.308951 CGGTCAACATTTGTTTCCCTATAAAGT 60.309 37.037 0.00 0.00 35.83 2.66
571 686 8.027189 GGTCAACATTTGTTTCCCTATAAAGTC 58.973 37.037 0.00 0.00 35.83 3.01
607 722 0.743688 ACCAAACAATGCGCAGTTGA 59.256 45.000 27.69 3.38 0.00 3.18
648 763 2.028112 TCTCGGTCAAACCCATCTGAAG 60.028 50.000 0.00 0.00 33.75 3.02
650 765 2.076863 CGGTCAAACCCATCTGAAGAC 58.923 52.381 0.00 0.00 33.75 3.01
666 781 1.710013 AGACGTCTATGCAAACACGG 58.290 50.000 18.46 2.57 36.56 4.94
668 783 1.296056 ACGTCTATGCAAACACGGCC 61.296 55.000 16.21 0.00 36.56 6.13
677 792 0.875728 CAAACACGGCCAAATCGGTA 59.124 50.000 2.24 0.00 36.97 4.02
715 830 9.407380 ACACATTAGACAAAATAGGATTATGCA 57.593 29.630 0.00 0.00 0.00 3.96
728 843 2.022764 TTATGCATCCGTCACCACAG 57.977 50.000 0.19 0.00 0.00 3.66
732 847 4.760047 ATCCGTCACCACAGCGCC 62.760 66.667 2.29 0.00 0.00 6.53
735 850 4.012895 CGTCACCACAGCGCCAAC 62.013 66.667 2.29 0.00 0.00 3.77
736 851 4.012895 GTCACCACAGCGCCAACG 62.013 66.667 2.29 0.00 44.07 4.10
791 917 3.844090 GGCGCTCCTCCTCCTCAC 61.844 72.222 7.64 0.00 0.00 3.51
839 968 4.251760 CGAACTGCTCGTCTGCTT 57.748 55.556 0.00 0.00 42.89 3.91
842 971 1.905922 GAACTGCTCGTCTGCTTGCC 61.906 60.000 0.00 0.00 0.00 4.52
845 974 4.704833 GCTCGTCTGCTTGCCCCA 62.705 66.667 0.00 0.00 0.00 4.96
931 1072 1.309499 CCTCGACGAGCTTGGAGACT 61.309 60.000 19.55 0.00 0.00 3.24
1041 1203 1.607628 GATCTGGTGATGCTGCATTCC 59.392 52.381 17.36 20.38 32.19 3.01
1070 1241 7.972832 CCTTTTTATTCTGCTGATTCCTTCTTC 59.027 37.037 0.00 0.00 0.00 2.87
1077 1248 2.355209 GCTGATTCCTTCTTCCTTCCGT 60.355 50.000 0.00 0.00 0.00 4.69
1197 1368 0.767375 TCTTGTCCTTTCTGCCTGCT 59.233 50.000 0.00 0.00 0.00 4.24
1302 1473 0.609681 AGTCGAGTTTCCCGAGCTCT 60.610 55.000 12.85 0.00 36.66 4.09
1344 1515 1.198713 AGCTCTTCATCCACATCCGT 58.801 50.000 0.00 0.00 0.00 4.69
1374 1545 2.037772 ACCTCTCGACAAGTGCAAGATT 59.962 45.455 0.00 0.00 0.00 2.40
1386 1557 1.881973 TGCAAGATTGTTGCCTGTCTC 59.118 47.619 15.12 0.00 44.32 3.36
1392 1563 1.795768 TTGTTGCCTGTCTCGATGAC 58.204 50.000 7.74 7.74 45.54 3.06
1416 1593 2.009774 GAGGAGCGCACATACACAAAT 58.990 47.619 11.47 0.00 0.00 2.32
1422 1599 3.694072 AGCGCACATACACAAATACCATT 59.306 39.130 11.47 0.00 0.00 3.16
1488 1692 3.081061 ACTCAGTGTTGCTGTTGACAAA 58.919 40.909 0.00 0.00 45.23 2.83
1503 1707 6.611381 TGTTGACAAAGACTTTGAGTTTGAG 58.389 36.000 30.01 5.63 43.26 3.02
1533 1737 1.068895 CTTGATGCGCCTCTCATCTCT 59.931 52.381 13.93 0.00 40.59 3.10
1560 1764 5.174395 CACTTGAAGATCCTACACCTTGAG 58.826 45.833 0.00 0.00 0.00 3.02
1564 1768 0.824759 GATCCTACACCTTGAGCGGT 59.175 55.000 0.00 0.00 37.93 5.68
1569 1773 2.489971 CTACACCTTGAGCGGTTTGAA 58.510 47.619 0.00 0.00 34.29 2.69
1570 1774 1.981256 ACACCTTGAGCGGTTTGAAT 58.019 45.000 0.00 0.00 34.29 2.57
2215 7358 7.903145 TGTAGTTCTGTCTTTCTTTATGCCTA 58.097 34.615 0.00 0.00 0.00 3.93
2235 7378 9.930158 ATGCCTAAAATTAAAGTATCTACCCAA 57.070 29.630 0.00 0.00 0.00 4.12
2236 7379 9.756571 TGCCTAAAATTAAAGTATCTACCCAAA 57.243 29.630 0.00 0.00 0.00 3.28
2842 8098 6.543100 TCACCGTAAGTAACCTTTGTCATTTT 59.457 34.615 0.00 0.00 31.89 1.82
3497 8979 5.627499 TGTTCAAGTTGCATGATAGTTCC 57.373 39.130 0.00 0.00 0.00 3.62
3514 8996 4.826556 AGTTCCTCTACATCAAACTGCTC 58.173 43.478 0.00 0.00 0.00 4.26
3538 9020 5.238583 GCCAAGCTATTATCCGTCTATGTT 58.761 41.667 0.00 0.00 0.00 2.71
3542 9024 7.542477 CCAAGCTATTATCCGTCTATGTTAGTG 59.458 40.741 0.00 0.00 0.00 2.74
3557 9039 8.772250 TCTATGTTAGTGGAGATCTTGGAATTT 58.228 33.333 0.00 0.00 0.00 1.82
3638 9120 1.987855 CCCTTGCCTCGGTCTACCA 60.988 63.158 0.00 0.00 35.14 3.25
3670 9152 0.037232 GACTCTCCAGTTTCCACCCG 60.037 60.000 0.00 0.00 30.63 5.28
3687 9169 1.416813 CCGTGACAGCGCTTGAGATC 61.417 60.000 7.50 0.87 0.00 2.75
3691 9173 1.276415 GACAGCGCTTGAGATCTGAC 58.724 55.000 7.50 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.125316 CAACATGCAAGAACAAACCTGG 58.875 45.455 0.00 0.00 0.00 4.45
8 9 2.540931 GCAACATGCAAGAACAAACCTG 59.459 45.455 0.00 0.00 44.26 4.00
75 76 0.323542 GTCACCTCTTCCTCCTCGGA 60.324 60.000 0.00 0.00 41.06 4.55
99 100 2.357569 GGCCATCAAGGTCAAGATCCTT 60.358 50.000 0.00 0.00 43.39 3.36
101 102 1.685148 GGCCATCAAGGTCAAGATCC 58.315 55.000 0.00 0.00 43.39 3.36
115 116 1.683365 GCCTCAACACCATGGCCAT 60.683 57.895 14.09 14.09 39.49 4.40
183 184 6.222038 TGTCTGACTTCTGTTATCCCATAC 57.778 41.667 9.51 0.00 0.00 2.39
238 254 3.403038 GTTGTTGCTTCCTCTTCTGCTA 58.597 45.455 0.00 0.00 0.00 3.49
260 344 6.207691 TCCTGTTTGTTTTCCTCTTCTTTG 57.792 37.500 0.00 0.00 0.00 2.77
262 346 5.714806 TGTTCCTGTTTGTTTTCCTCTTCTT 59.285 36.000 0.00 0.00 0.00 2.52
275 359 4.326009 CGTTGTTCCTTTTGTTCCTGTTTG 59.674 41.667 0.00 0.00 0.00 2.93
276 360 4.490743 CGTTGTTCCTTTTGTTCCTGTTT 58.509 39.130 0.00 0.00 0.00 2.83
278 362 2.425668 CCGTTGTTCCTTTTGTTCCTGT 59.574 45.455 0.00 0.00 0.00 4.00
279 363 2.685897 TCCGTTGTTCCTTTTGTTCCTG 59.314 45.455 0.00 0.00 0.00 3.86
280 364 3.007473 TCCGTTGTTCCTTTTGTTCCT 57.993 42.857 0.00 0.00 0.00 3.36
281 365 3.379057 TCTTCCGTTGTTCCTTTTGTTCC 59.621 43.478 0.00 0.00 0.00 3.62
282 366 4.497507 CCTCTTCCGTTGTTCCTTTTGTTC 60.498 45.833 0.00 0.00 0.00 3.18
283 367 3.380320 CCTCTTCCGTTGTTCCTTTTGTT 59.620 43.478 0.00 0.00 0.00 2.83
284 368 2.949644 CCTCTTCCGTTGTTCCTTTTGT 59.050 45.455 0.00 0.00 0.00 2.83
285 369 2.949644 ACCTCTTCCGTTGTTCCTTTTG 59.050 45.455 0.00 0.00 0.00 2.44
286 370 3.292492 ACCTCTTCCGTTGTTCCTTTT 57.708 42.857 0.00 0.00 0.00 2.27
287 371 4.102054 TCTTACCTCTTCCGTTGTTCCTTT 59.898 41.667 0.00 0.00 0.00 3.11
288 372 3.644738 TCTTACCTCTTCCGTTGTTCCTT 59.355 43.478 0.00 0.00 0.00 3.36
289 373 3.236896 TCTTACCTCTTCCGTTGTTCCT 58.763 45.455 0.00 0.00 0.00 3.36
290 374 3.257624 TCTCTTACCTCTTCCGTTGTTCC 59.742 47.826 0.00 0.00 0.00 3.62
291 375 4.516365 TCTCTTACCTCTTCCGTTGTTC 57.484 45.455 0.00 0.00 0.00 3.18
292 376 4.950205 TTCTCTTACCTCTTCCGTTGTT 57.050 40.909 0.00 0.00 0.00 2.83
293 377 4.587684 TCTTTCTCTTACCTCTTCCGTTGT 59.412 41.667 0.00 0.00 0.00 3.32
294 378 5.135508 TCTTTCTCTTACCTCTTCCGTTG 57.864 43.478 0.00 0.00 0.00 4.10
295 379 5.539193 TCTTCTTTCTCTTACCTCTTCCGTT 59.461 40.000 0.00 0.00 0.00 4.44
296 380 5.078256 TCTTCTTTCTCTTACCTCTTCCGT 58.922 41.667 0.00 0.00 0.00 4.69
297 381 5.393678 CCTCTTCTTTCTCTTACCTCTTCCG 60.394 48.000 0.00 0.00 0.00 4.30
298 382 5.105106 CCCTCTTCTTTCTCTTACCTCTTCC 60.105 48.000 0.00 0.00 0.00 3.46
299 383 5.717654 TCCCTCTTCTTTCTCTTACCTCTTC 59.282 44.000 0.00 0.00 0.00 2.87
300 384 5.656420 TCCCTCTTCTTTCTCTTACCTCTT 58.344 41.667 0.00 0.00 0.00 2.85
301 385 5.278127 TCCCTCTTCTTTCTCTTACCTCT 57.722 43.478 0.00 0.00 0.00 3.69
302 386 5.659079 TCATCCCTCTTCTTTCTCTTACCTC 59.341 44.000 0.00 0.00 0.00 3.85
303 387 5.594777 TCATCCCTCTTCTTTCTCTTACCT 58.405 41.667 0.00 0.00 0.00 3.08
304 388 5.941555 TCATCCCTCTTCTTTCTCTTACC 57.058 43.478 0.00 0.00 0.00 2.85
305 389 7.118496 TCATCATCCCTCTTCTTTCTCTTAC 57.882 40.000 0.00 0.00 0.00 2.34
306 390 7.401493 AGTTCATCATCCCTCTTCTTTCTCTTA 59.599 37.037 0.00 0.00 0.00 2.10
317 409 5.261040 TGGAAAAAGTTCATCATCCCTCT 57.739 39.130 0.00 0.00 35.25 3.69
382 495 6.827727 ACAAATTACGGTTCATCCTAGCTAT 58.172 36.000 0.00 0.00 0.00 2.97
432 546 3.007506 TGATGACCTTACCACACACGATT 59.992 43.478 0.00 0.00 0.00 3.34
452 566 4.202121 GGTGTCACAACTTCTCACTAGTGA 60.202 45.833 23.80 23.80 38.06 3.41
467 581 3.495331 ACCTGCATTAAATGGTGTCACA 58.505 40.909 5.12 0.00 0.00 3.58
524 638 1.040646 TTGTTTGGTTGGCCGCATAA 58.959 45.000 0.00 0.00 37.67 1.90
543 657 2.661718 AGGGAAACAAATGTTGACCGT 58.338 42.857 0.00 5.99 38.71 4.83
559 674 9.417561 CCCGTATATAGATTGACTTTATAGGGA 57.582 37.037 18.22 0.00 44.31 4.20
566 681 8.253867 TGGTTACCCGTATATAGATTGACTTT 57.746 34.615 0.00 0.00 0.00 2.66
567 682 7.844493 TGGTTACCCGTATATAGATTGACTT 57.156 36.000 0.00 0.00 0.00 3.01
570 685 8.020777 TGTTTGGTTACCCGTATATAGATTGA 57.979 34.615 0.00 0.00 0.00 2.57
571 686 8.665643 TTGTTTGGTTACCCGTATATAGATTG 57.334 34.615 0.00 0.00 0.00 2.67
581 696 0.594110 CGCATTGTTTGGTTACCCGT 59.406 50.000 0.00 0.00 0.00 5.28
599 714 3.002656 CAGCCTATAAACCATCAACTGCG 59.997 47.826 0.00 0.00 0.00 5.18
631 746 2.076863 CGTCTTCAGATGGGTTTGACC 58.923 52.381 0.00 0.00 37.60 4.02
636 751 3.430929 GCATAGACGTCTTCAGATGGGTT 60.431 47.826 25.44 0.00 35.43 4.11
648 763 0.094730 GCCGTGTTTGCATAGACGTC 59.905 55.000 21.64 7.70 0.00 4.34
650 765 1.295357 TGGCCGTGTTTGCATAGACG 61.295 55.000 17.79 17.79 0.00 4.18
666 781 2.041686 TTGCCCGTACCGATTTGGC 61.042 57.895 0.00 0.00 43.94 4.52
668 783 0.956410 TGGTTGCCCGTACCGATTTG 60.956 55.000 0.00 0.00 38.55 2.32
677 792 1.611491 CTAATGTGTTTGGTTGCCCGT 59.389 47.619 0.00 0.00 0.00 5.28
711 826 1.746615 GCTGTGGTGACGGATGCAT 60.747 57.895 0.00 0.00 0.00 3.96
714 829 3.490759 GCGCTGTGGTGACGGATG 61.491 66.667 0.00 0.00 0.00 3.51
715 830 4.760047 GGCGCTGTGGTGACGGAT 62.760 66.667 7.64 0.00 0.00 4.18
732 847 4.715892 AAAATGGCCGCGGCGTTG 62.716 61.111 41.05 9.78 43.06 4.10
733 848 4.413800 GAAAATGGCCGCGGCGTT 62.414 61.111 41.05 33.55 43.06 4.84
736 851 2.763627 AAAGTGAAAATGGCCGCGGC 62.764 55.000 41.63 41.63 41.06 6.53
737 852 0.732538 GAAAGTGAAAATGGCCGCGG 60.733 55.000 24.05 24.05 0.00 6.46
778 904 1.930251 TCAACAGTGAGGAGGAGGAG 58.070 55.000 0.00 0.00 0.00 3.69
779 905 2.398754 TTCAACAGTGAGGAGGAGGA 57.601 50.000 0.00 0.00 34.49 3.71
780 906 2.093235 GGATTCAACAGTGAGGAGGAGG 60.093 54.545 0.00 0.00 34.49 4.30
791 917 2.046285 GTGGGGCGGGATTCAACAG 61.046 63.158 0.00 0.00 0.00 3.16
1041 1203 4.100035 GGAATCAGCAGAATAAAAAGGGGG 59.900 45.833 0.00 0.00 0.00 5.40
1045 1207 7.972832 GGAAGAAGGAATCAGCAGAATAAAAAG 59.027 37.037 0.00 0.00 0.00 2.27
1051 1222 4.858965 AGGAAGAAGGAATCAGCAGAAT 57.141 40.909 0.00 0.00 0.00 2.40
1179 1350 0.879765 CAGCAGGCAGAAAGGACAAG 59.120 55.000 0.00 0.00 0.00 3.16
1180 1351 1.174712 GCAGCAGGCAGAAAGGACAA 61.175 55.000 0.00 0.00 43.97 3.18
1197 1368 2.045634 GTCTGCAGGGCATCAGCA 60.046 61.111 15.13 0.00 44.61 4.41
1302 1473 2.088423 ACCAGCTGTTTGAAACGTTCA 58.912 42.857 13.81 0.00 38.04 3.18
1339 1510 0.252284 AGAGGTGAGTTCCCACGGAT 60.252 55.000 0.00 0.00 37.91 4.18
1344 1515 0.178973 TGTCGAGAGGTGAGTTCCCA 60.179 55.000 0.00 0.00 0.00 4.37
1374 1545 3.514777 GTCATCGAGACAGGCAACA 57.485 52.632 9.30 0.00 46.77 3.33
1386 1557 2.278206 CGCTCCTCCACGTCATCG 60.278 66.667 0.00 0.00 43.34 3.84
1392 1563 1.878522 GTATGTGCGCTCCTCCACG 60.879 63.158 9.73 0.00 34.77 4.94
1394 1565 1.218047 GTGTATGTGCGCTCCTCCA 59.782 57.895 9.73 0.00 0.00 3.86
1416 1593 4.732647 GCGTACTCGATCAACAGAATGGTA 60.733 45.833 0.00 0.00 39.18 3.25
1488 1692 3.567478 AGTGGCTCAAACTCAAAGTCT 57.433 42.857 0.00 0.00 0.00 3.24
1503 1707 1.264288 GGCGCATCAAGTATTAGTGGC 59.736 52.381 10.83 0.00 0.00 5.01
1533 1737 3.055819 GGTGTAGGATCTTCAAGTGCTGA 60.056 47.826 0.00 0.00 0.00 4.26
1560 1764 2.659757 GGAGCGTTTTAATTCAAACCGC 59.340 45.455 16.94 16.94 36.89 5.68
1564 1768 5.529430 TCAGAGTGGAGCGTTTTAATTCAAA 59.471 36.000 0.00 0.00 0.00 2.69
1569 1773 6.431234 AGAAATTCAGAGTGGAGCGTTTTAAT 59.569 34.615 0.00 0.00 0.00 1.40
1570 1774 5.763204 AGAAATTCAGAGTGGAGCGTTTTAA 59.237 36.000 0.00 0.00 0.00 1.52
2215 7358 9.251440 GGGACTTTGGGTAGATACTTTAATTTT 57.749 33.333 0.00 0.00 0.00 1.82
2236 7379 2.711547 AGTAAGCAGGAAGTTTGGGACT 59.288 45.455 0.00 0.00 41.47 3.85
2237 7380 3.141767 AGTAAGCAGGAAGTTTGGGAC 57.858 47.619 0.00 0.00 0.00 4.46
2238 7381 3.876309 AAGTAAGCAGGAAGTTTGGGA 57.124 42.857 0.00 0.00 0.00 4.37
2239 7382 6.590234 ATTTAAGTAAGCAGGAAGTTTGGG 57.410 37.500 0.00 0.00 0.00 4.12
2251 7394 6.379386 AGAAGGCGAAACAATTTAAGTAAGC 58.621 36.000 0.00 0.00 0.00 3.09
2651 7867 4.000988 TCCTGTTGCTCTAACGAATTTCC 58.999 43.478 0.00 0.00 42.34 3.13
3221 8693 5.768164 TCACCCCTCAGTTGAAGATTTTTAC 59.232 40.000 0.00 0.00 0.00 2.01
3473 8955 6.072286 AGGAACTATCATGCAACTTGAACAAG 60.072 38.462 12.22 12.22 40.17 3.16
3497 8979 1.929836 GGCGAGCAGTTTGATGTAGAG 59.070 52.381 0.00 0.00 0.00 2.43
3514 8996 2.440539 AGACGGATAATAGCTTGGCG 57.559 50.000 0.00 0.00 0.00 5.69
3538 9020 6.659242 GGTTTCAAATTCCAAGATCTCCACTA 59.341 38.462 0.00 0.00 0.00 2.74
3542 9024 5.982890 TGGTTTCAAATTCCAAGATCTCC 57.017 39.130 0.00 0.00 0.00 3.71
3557 9039 5.009110 TGACGATGCAATAAGTTTGGTTTCA 59.991 36.000 0.00 0.00 0.00 2.69
3638 9120 3.692406 GAGTCCGCCTGGTTCCGT 61.692 66.667 0.00 0.00 36.30 4.69
3670 9152 0.997932 CAGATCTCAAGCGCTGTCAC 59.002 55.000 12.58 0.64 0.00 3.67
3687 9169 0.165295 CACAAGCGAGCATGTGTCAG 59.835 55.000 20.94 0.67 39.77 3.51
3691 9173 0.098200 CCATCACAAGCGAGCATGTG 59.902 55.000 22.57 22.57 44.14 3.21


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

AutoCloner maintained by Alex Coulton.