Multiple sequence alignment - TraesCS2D01G209600

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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 TraesCS2D01G209600 chr2D 100.000 3266 0 0 1 3266 165469498 165466233 0.000000e+00 6032.0
1 TraesCS2D01G209600 chr2D 85.517 145 21 0 1235 1379 471055953 471055809 5.640000e-33 152.0
2 TraesCS2D01G209600 chr2D 85.294 136 16 4 1240 1373 417625369 417625502 1.580000e-28 137.0
3 TraesCS2D01G209600 chr2A 91.195 3305 144 71 69 3266 185283832 185287096 0.000000e+00 4355.0
4 TraesCS2D01G209600 chr2A 85.714 140 20 0 1240 1379 612835028 612834889 7.300000e-32 148.0
5 TraesCS2D01G209600 chr2A 84.892 139 17 4 1240 1376 572487553 572487417 1.580000e-28 137.0
6 TraesCS2D01G209600 chr2A 90.541 74 4 1 1 74 185283748 185283818 9.650000e-16 95.3
7 TraesCS2D01G209600 chr7D 75.410 366 59 22 1256 1615 13098015 13097675 7.300000e-32 148.0
8 TraesCS2D01G209600 chr7D 84.783 138 19 2 1479 1615 13029169 13029033 1.580000e-28 137.0
9 TraesCS2D01G209600 chr7D 84.783 138 19 2 1479 1615 13066900 13066764 1.580000e-28 137.0
10 TraesCS2D01G209600 chr2B 86.614 127 17 0 1253 1379 550214166 550214040 1.220000e-29 141.0
11 TraesCS2D01G209600 chr2B 85.185 135 16 4 1241 1373 489849194 489849326 5.680000e-28 135.0
12 TraesCS2D01G209600 chr7A 84.783 138 19 2 1479 1615 12454993 12454857 1.580000e-28 137.0
13 TraesCS2D01G209600 chr7A 84.672 137 19 2 1480 1615 12652387 12652252 5.680000e-28 135.0
14 TraesCS2D01G209600 chr7A 83.333 138 21 2 1479 1615 12429304 12429168 3.420000e-25 126.0
15 TraesCS2D01G209600 chr4A 84.783 138 19 2 1479 1615 724782969 724783105 1.580000e-28 137.0
16 TraesCS2D01G209600 chr5A 86.885 122 12 4 1253 1372 414934545 414934426 2.040000e-27 134.0
17 TraesCS2D01G209600 chr5D 86.179 123 13 4 1253 1373 319254580 319254700 2.640000e-26 130.0
18 TraesCS2D01G209600 chr4D 84.496 129 18 2 1479 1606 506606765 506606638 3.420000e-25 126.0
19 TraesCS2D01G209600 chr1D 84.416 77 12 0 998 1074 459880645 459880569 3.490000e-10 76.8
20 TraesCS2D01G209600 chr1A 84.416 77 12 0 998 1074 551593139 551593063 3.490000e-10 76.8


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 TraesCS2D01G209600 chr2D 165466233 165469498 3265 True 6032.00 6032 100.000 1 3266 1 chr2D.!!$R1 3265
1 TraesCS2D01G209600 chr2A 185283748 185287096 3348 False 2225.15 4355 90.868 1 3266 2 chr2A.!!$F1 3265

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
660 698 0.179045 CCATCCTCATCCAACGGACC 60.179 60.0 0.0 0.0 32.98 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 2497 0.308068 CGGCTCTCGTACGTGATCAT 59.692 55.0 19.21 0.0 0.0 2.45 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
28 29 2.187946 CCACGAGGGCTTGCTAGG 59.812 66.667 0.00 0.00 0.00 3.02
33 34 0.605589 CGAGGGCTTGCTAGGGATAG 59.394 60.000 0.00 0.00 0.00 2.08
34 35 1.823648 CGAGGGCTTGCTAGGGATAGA 60.824 57.143 0.00 0.00 0.00 1.98
35 36 2.545810 GAGGGCTTGCTAGGGATAGAT 58.454 52.381 0.00 0.00 0.00 1.98
175 195 1.295792 GAGTGGCAAAACACGAGTCA 58.704 50.000 0.00 0.00 45.80 3.41
182 202 4.088648 GGCAAAACACGAGTCAAATATCG 58.911 43.478 0.00 0.00 44.36 2.92
185 205 6.237996 GGCAAAACACGAGTCAAATATCGATA 60.238 38.462 7.75 7.75 41.40 2.92
229 255 1.551452 CCCGCCAAGAAATTTACCCA 58.449 50.000 0.00 0.00 0.00 4.51
230 256 1.203758 CCCGCCAAGAAATTTACCCAC 59.796 52.381 0.00 0.00 0.00 4.61
231 257 2.167662 CCGCCAAGAAATTTACCCACT 58.832 47.619 0.00 0.00 0.00 4.00
232 258 3.349022 CCGCCAAGAAATTTACCCACTA 58.651 45.455 0.00 0.00 0.00 2.74
234 260 4.007659 CGCCAAGAAATTTACCCACTACT 58.992 43.478 0.00 0.00 0.00 2.57
235 261 5.180271 CGCCAAGAAATTTACCCACTACTA 58.820 41.667 0.00 0.00 0.00 1.82
236 262 5.064325 CGCCAAGAAATTTACCCACTACTAC 59.936 44.000 0.00 0.00 0.00 2.73
240 266 7.490402 CCAAGAAATTTACCCACTACTACGTAG 59.510 40.741 20.97 20.97 41.43 3.51
250 276 4.643784 CCACTACTACGTAGATCCTTGGTT 59.356 45.833 28.74 5.72 38.29 3.67
253 279 7.192232 CACTACTACGTAGATCCTTGGTTTAC 58.808 42.308 28.74 0.00 38.29 2.01
310 336 4.232221 CTGTTTTGCACTCCATCATTGTC 58.768 43.478 0.00 0.00 0.00 3.18
361 394 4.448395 CGGAGTCTAGTAGATTCTACCACG 59.552 50.000 18.88 11.49 32.30 4.94
382 415 3.790820 CGATCGGTAAAAATGGCATGTTG 59.209 43.478 7.38 0.00 0.00 3.33
393 426 0.179156 GGCATGTTGCTGATGGAACG 60.179 55.000 0.00 0.00 45.68 3.95
400 433 0.825425 TGCTGATGGAACGGGCAAAA 60.825 50.000 0.00 0.00 0.00 2.44
403 436 1.215382 GATGGAACGGGCAAAAGGC 59.785 57.895 0.00 0.00 43.74 4.35
412 445 3.380995 GCAAAAGGCCAAGGGAGG 58.619 61.111 5.01 0.00 36.11 4.30
413 446 1.228862 GCAAAAGGCCAAGGGAGGA 60.229 57.895 5.01 0.00 36.11 3.71
414 447 1.253593 GCAAAAGGCCAAGGGAGGAG 61.254 60.000 5.01 0.00 36.11 3.69
415 448 0.613012 CAAAAGGCCAAGGGAGGAGG 60.613 60.000 5.01 0.00 0.00 4.30
416 449 0.776080 AAAAGGCCAAGGGAGGAGGA 60.776 55.000 5.01 0.00 0.00 3.71
417 450 0.776080 AAAGGCCAAGGGAGGAGGAA 60.776 55.000 5.01 0.00 0.00 3.36
418 451 1.210885 AAGGCCAAGGGAGGAGGAAG 61.211 60.000 5.01 0.00 0.00 3.46
419 452 2.273776 GCCAAGGGAGGAGGAAGC 59.726 66.667 0.00 0.00 0.00 3.86
420 453 2.606587 GCCAAGGGAGGAGGAAGCA 61.607 63.158 0.00 0.00 0.00 3.91
421 454 1.301293 CCAAGGGAGGAGGAAGCAC 59.699 63.158 0.00 0.00 0.00 4.40
422 455 1.078848 CAAGGGAGGAGGAAGCACG 60.079 63.158 0.00 0.00 0.00 5.34
423 456 2.960688 AAGGGAGGAGGAAGCACGC 61.961 63.158 0.00 0.00 0.00 5.34
424 457 3.394836 GGGAGGAGGAAGCACGCT 61.395 66.667 0.00 0.00 0.00 5.07
425 458 2.185608 GGAGGAGGAAGCACGCTC 59.814 66.667 0.00 0.00 0.00 5.03
426 459 2.185608 GAGGAGGAAGCACGCTCC 59.814 66.667 0.00 0.00 36.72 4.70
427 460 2.604686 AGGAGGAAGCACGCTCCA 60.605 61.111 0.00 0.00 37.96 3.86
428 461 2.435059 GGAGGAAGCACGCTCCAC 60.435 66.667 0.00 4.23 36.58 4.02
429 462 2.659610 GAGGAAGCACGCTCCACT 59.340 61.111 9.28 1.29 0.00 4.00
430 463 1.739562 GAGGAAGCACGCTCCACTG 60.740 63.158 9.28 0.00 0.00 3.66
431 464 2.159819 GAGGAAGCACGCTCCACTGA 62.160 60.000 9.28 0.00 0.00 3.41
465 498 5.798125 AGGATCGACACATGTGATTATCT 57.202 39.130 31.94 17.09 0.00 1.98
466 499 5.777802 AGGATCGACACATGTGATTATCTC 58.222 41.667 31.94 16.22 0.00 2.75
467 500 4.618912 GGATCGACACATGTGATTATCTCG 59.381 45.833 31.94 25.96 0.00 4.04
478 515 5.301555 TGTGATTATCTCGGTCAAAACACA 58.698 37.500 0.00 0.00 33.30 3.72
489 526 4.499040 CGGTCAAAACACAAGACAATGTTC 59.501 41.667 0.00 0.00 38.08 3.18
494 531 2.912771 ACACAAGACAATGTTCCACGA 58.087 42.857 0.00 0.00 0.00 4.35
572 609 3.790437 CGTGGGATCTGCCTGGCT 61.790 66.667 21.03 0.00 36.66 4.75
660 698 0.179045 CCATCCTCATCCAACGGACC 60.179 60.000 0.00 0.00 32.98 4.46
666 704 2.100631 CATCCAACGGACCAGACGC 61.101 63.158 0.00 0.00 32.98 5.19
668 706 1.827399 ATCCAACGGACCAGACGCTT 61.827 55.000 0.00 0.00 32.98 4.68
669 707 1.597027 CCAACGGACCAGACGCTTT 60.597 57.895 0.00 0.00 34.00 3.51
671 709 1.301479 AACGGACCAGACGCTTTCC 60.301 57.895 0.00 0.00 34.00 3.13
672 710 2.809601 CGGACCAGACGCTTTCCG 60.810 66.667 10.31 10.31 44.65 4.30
822 860 2.650322 CGCCCTTTATAAGCCTTTCCA 58.350 47.619 0.00 0.00 0.00 3.53
870 908 0.605589 CTCTACCTCCATCCATCCGC 59.394 60.000 0.00 0.00 0.00 5.54
917 960 3.080300 GCTAGCTAGCTCCTCTCCATA 57.920 52.381 33.71 0.00 45.62 2.74
921 964 2.167662 GCTAGCTCCTCTCCATACTCC 58.832 57.143 7.70 0.00 0.00 3.85
953 1001 2.363359 CAAACTGAGCCTTTTCCTGCTT 59.637 45.455 0.00 0.00 38.11 3.91
955 1003 1.133668 ACTGAGCCTTTTCCTGCTTGT 60.134 47.619 0.00 0.00 38.11 3.16
956 1004 1.959282 CTGAGCCTTTTCCTGCTTGTT 59.041 47.619 0.00 0.00 38.11 2.83
979 1027 0.681887 TCGCCCAATCCGTCTCTACA 60.682 55.000 0.00 0.00 0.00 2.74
980 1028 0.249073 CGCCCAATCCGTCTCTACAG 60.249 60.000 0.00 0.00 0.00 2.74
982 1030 1.207329 GCCCAATCCGTCTCTACAGTT 59.793 52.381 0.00 0.00 0.00 3.16
984 1032 2.761208 CCCAATCCGTCTCTACAGTTCT 59.239 50.000 0.00 0.00 0.00 3.01
985 1033 3.195825 CCCAATCCGTCTCTACAGTTCTT 59.804 47.826 0.00 0.00 0.00 2.52
986 1034 4.177026 CCAATCCGTCTCTACAGTTCTTG 58.823 47.826 0.00 0.00 0.00 3.02
1075 1125 0.681564 GGAGGAGGACGAGAAGCTCA 60.682 60.000 0.00 0.00 0.00 4.26
1151 1201 0.179169 GGTAAGCGACTCGGACTCAC 60.179 60.000 0.00 0.00 0.00 3.51
1152 1202 0.520404 GTAAGCGACTCGGACTCACA 59.480 55.000 0.00 0.00 0.00 3.58
1190 1260 0.611200 ACCGATCGATCCCACACAAA 59.389 50.000 18.66 0.00 0.00 2.83
1191 1261 1.290203 CCGATCGATCCCACACAAAG 58.710 55.000 18.66 2.24 0.00 2.77
1192 1262 1.290203 CGATCGATCCCACACAAAGG 58.710 55.000 19.51 0.00 0.00 3.11
1233 1303 0.531974 ATCGGTTGTGTTGCGTCTGT 60.532 50.000 0.00 0.00 0.00 3.41
1248 1318 0.179076 TCTGTGTGTGTGCAGACCTG 60.179 55.000 12.00 0.70 38.02 4.00
1353 1423 1.344114 GAGGAGACCATCATCCAGCTC 59.656 57.143 0.00 0.00 38.12 4.09
1383 1453 3.575256 TCCTCGGCAACAAGTAAGAACTA 59.425 43.478 0.00 0.00 33.75 2.24
1384 1454 3.678548 CCTCGGCAACAAGTAAGAACTAC 59.321 47.826 0.00 0.00 33.75 2.73
1385 1455 3.311106 TCGGCAACAAGTAAGAACTACG 58.689 45.455 0.00 0.00 33.75 3.51
1386 1456 3.054878 CGGCAACAAGTAAGAACTACGT 58.945 45.455 0.00 0.00 33.75 3.57
1387 1457 4.023279 TCGGCAACAAGTAAGAACTACGTA 60.023 41.667 0.00 0.00 33.75 3.57
1388 1458 4.681025 CGGCAACAAGTAAGAACTACGTAA 59.319 41.667 0.00 0.00 33.75 3.18
1389 1459 5.346822 CGGCAACAAGTAAGAACTACGTAAT 59.653 40.000 0.00 0.00 33.75 1.89
1390 1460 6.128742 CGGCAACAAGTAAGAACTACGTAATT 60.129 38.462 0.00 0.00 33.75 1.40
1391 1461 7.062138 CGGCAACAAGTAAGAACTACGTAATTA 59.938 37.037 0.00 0.00 33.75 1.40
1392 1462 8.711457 GGCAACAAGTAAGAACTACGTAATTAA 58.289 33.333 0.00 0.00 33.75 1.40
1393 1463 9.521179 GCAACAAGTAAGAACTACGTAATTAAC 57.479 33.333 0.00 0.00 33.75 2.01
1456 1573 1.164041 ACGGTTTCCTGGCGAGTTTG 61.164 55.000 0.00 0.00 0.00 2.93
1457 1574 1.852067 CGGTTTCCTGGCGAGTTTGG 61.852 60.000 0.00 0.00 0.00 3.28
1468 1592 5.263968 TGGCGAGTTTGGTTTTGATTTTA 57.736 34.783 0.00 0.00 0.00 1.52
1659 1783 4.217159 GCCGCCTACTACCCCACG 62.217 72.222 0.00 0.00 0.00 4.94
1948 2072 1.066858 AGCAACTACACCAGGATCACG 60.067 52.381 0.00 0.00 0.00 4.35
2155 2282 1.495584 GCGTGTGAACTCGGCTTCAA 61.496 55.000 6.99 0.00 31.90 2.69
2158 2285 0.878523 TGTGAACTCGGCTTCAACGG 60.879 55.000 0.00 0.00 31.90 4.44
2161 2288 1.901650 GAACTCGGCTTCAACGGCAG 61.902 60.000 0.00 0.00 0.00 4.85
2184 2311 2.969806 CTGCGCCAACACGAGCAAT 61.970 57.895 4.18 0.00 39.26 3.56
2187 2314 0.098728 GCGCCAACACGAGCAATATT 59.901 50.000 0.00 0.00 34.06 1.28
2265 2392 3.066760 TGGATGTGAGCGACTACATGTAG 59.933 47.826 27.66 27.66 37.63 2.74
2289 2417 5.413523 GTGAAAATACAAGTACGGGTTCCAT 59.586 40.000 0.00 0.00 0.00 3.41
2290 2418 6.005198 TGAAAATACAAGTACGGGTTCCATT 58.995 36.000 0.00 0.00 0.00 3.16
2291 2419 6.149807 TGAAAATACAAGTACGGGTTCCATTC 59.850 38.462 0.00 0.00 0.00 2.67
2292 2420 2.484742 ACAAGTACGGGTTCCATTCC 57.515 50.000 0.00 0.00 0.00 3.01
2293 2421 1.700739 ACAAGTACGGGTTCCATTCCA 59.299 47.619 0.00 0.00 0.00 3.53
2294 2422 2.081462 CAAGTACGGGTTCCATTCCAC 58.919 52.381 0.00 0.00 0.00 4.02
2295 2423 1.354101 AGTACGGGTTCCATTCCACA 58.646 50.000 0.00 0.00 0.00 4.17
2315 2444 4.112716 CATGCATGCATGTGGAAACTAA 57.887 40.909 40.30 10.04 46.20 2.24
2318 2447 3.573538 TGCATGCATGTGGAAACTAAGTT 59.426 39.130 26.79 0.00 0.00 2.66
2334 2463 5.357257 ACTAAGTTGAACAGTTCATCACGT 58.643 37.500 21.38 15.80 39.84 4.49
2335 2464 6.509656 ACTAAGTTGAACAGTTCATCACGTA 58.490 36.000 21.38 16.02 39.84 3.57
2336 2465 5.652744 AAGTTGAACAGTTCATCACGTAC 57.347 39.130 21.38 13.91 39.84 3.67
2347 2476 1.004185 CATCACGTACTACCGACCGAG 60.004 57.143 0.00 0.00 0.00 4.63
2361 2490 2.429930 CGAGAGGGGGCAAACACA 59.570 61.111 0.00 0.00 0.00 3.72
2362 2491 1.002134 CGAGAGGGGGCAAACACAT 60.002 57.895 0.00 0.00 0.00 3.21
2363 2492 1.308069 CGAGAGGGGGCAAACACATG 61.308 60.000 0.00 0.00 0.00 3.21
2364 2493 1.598701 GAGAGGGGGCAAACACATGC 61.599 60.000 0.00 0.00 45.67 4.06
2374 2503 3.776340 GCAAACACATGCATGATGATCA 58.224 40.909 32.75 0.00 45.70 2.92
2375 2504 3.550275 GCAAACACATGCATGATGATCAC 59.450 43.478 32.75 12.24 45.70 3.06
2376 2505 3.685836 AACACATGCATGATGATCACG 57.314 42.857 32.75 11.88 35.80 4.35
2377 2506 2.635714 ACACATGCATGATGATCACGT 58.364 42.857 32.75 12.45 35.80 4.49
2455 2588 7.827729 ACTGGTTACTGTTAGAAACTTCACTTT 59.172 33.333 0.00 0.00 0.00 2.66
2458 2591 7.431376 GGTTACTGTTAGAAACTTCACTTTTGC 59.569 37.037 0.00 0.00 0.00 3.68
2623 2756 5.770162 CCAGTGAAGAAAAATAGGGTCACTT 59.230 40.000 1.51 0.00 42.19 3.16
2624 2757 6.294176 CCAGTGAAGAAAAATAGGGTCACTTG 60.294 42.308 1.51 0.00 42.19 3.16
2625 2758 5.241728 AGTGAAGAAAAATAGGGTCACTTGC 59.758 40.000 0.00 0.00 42.19 4.01
2626 2759 5.009610 GTGAAGAAAAATAGGGTCACTTGCA 59.990 40.000 0.00 0.00 34.05 4.08
2628 2761 5.904362 AGAAAAATAGGGTCACTTGCATC 57.096 39.130 0.00 0.00 0.00 3.91
2629 2762 5.324409 AGAAAAATAGGGTCACTTGCATCA 58.676 37.500 0.00 0.00 0.00 3.07
2630 2763 5.954150 AGAAAAATAGGGTCACTTGCATCAT 59.046 36.000 0.00 0.00 0.00 2.45
2631 2764 7.118723 AGAAAAATAGGGTCACTTGCATCATA 58.881 34.615 0.00 0.00 0.00 2.15
2685 2840 8.421002 TCTTTAGTTTAATTTTGCTGCCTCTTT 58.579 29.630 0.00 0.00 0.00 2.52
2707 2862 9.575868 TCTTTTATTTCATTGGTTACTGTACCA 57.424 29.630 5.41 5.41 46.23 3.25
2716 2871 7.179516 TCATTGGTTACTGTACCACTGAGAATA 59.820 37.037 17.26 4.59 46.62 1.75
2825 2980 7.092716 GGTCACATGACAAGCAATTATTCTTT 58.907 34.615 13.77 0.00 46.47 2.52
2856 3011 3.440522 GGAAAATAGACTGGAGTTGGTGC 59.559 47.826 0.00 0.00 0.00 5.01
2867 3022 2.584791 GAGTTGGTGCGCAACTTAATG 58.415 47.619 28.12 0.00 42.28 1.90
2895 3051 2.024871 CCTGCTCCGTCGATCGAC 59.975 66.667 33.22 33.22 42.86 4.20
2918 3074 1.942586 GCGACCAACAGTTACCCGATT 60.943 52.381 0.00 0.00 0.00 3.34
2942 3100 7.106439 TGACCACATGTATTTGTTTTTCTGT 57.894 32.000 0.00 0.00 0.00 3.41
2943 3101 8.226819 TGACCACATGTATTTGTTTTTCTGTA 57.773 30.769 0.00 0.00 0.00 2.74
2944 3102 8.855110 TGACCACATGTATTTGTTTTTCTGTAT 58.145 29.630 0.00 0.00 0.00 2.29
3080 3242 0.461163 TGGTCAGGTCAACACACACG 60.461 55.000 0.00 0.00 0.00 4.49
3114 3279 1.954382 TGCATGAGCCTAGGTAGTACG 59.046 52.381 11.31 0.00 41.13 3.67
3118 3283 1.064166 TGAGCCTAGGTAGTACGCCTT 60.064 52.381 11.31 0.32 37.54 4.35
3147 3312 5.165676 CCAATGTGTGTAGTGTACGTACAT 58.834 41.667 29.58 20.02 38.57 2.29
3159 3324 6.038356 AGTGTACGTACATACATACCAAAGC 58.962 40.000 29.58 12.86 37.40 3.51
3173 3338 6.434028 ACATACCAAAGCAACTCAATGTATGT 59.566 34.615 0.00 0.00 41.37 2.29
3193 3358 9.135843 TGTATGTATGCATTCTTAGTTATACGC 57.864 33.333 3.54 0.00 36.58 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.016905 TCTATCCCTAGCAAGCCCTC 57.983 55.000 0.00 0.00 0.00 4.30
21 22 4.528596 GCCAACTCTATCTATCCCTAGCAA 59.471 45.833 0.00 0.00 0.00 3.91
22 23 4.090090 GCCAACTCTATCTATCCCTAGCA 58.910 47.826 0.00 0.00 0.00 3.49
28 29 1.550976 CCCGGCCAACTCTATCTATCC 59.449 57.143 2.24 0.00 0.00 2.59
104 124 4.290622 CCTGCCCTGCCTTGTGGT 62.291 66.667 0.00 0.00 35.27 4.16
122 142 4.072088 GTTGACGAACGCCGCTGG 62.072 66.667 0.00 0.00 43.32 4.85
163 183 8.873215 ATCTATCGATATTTGACTCGTGTTTT 57.127 30.769 5.40 0.00 36.33 2.43
185 205 6.016777 GCGAAACATCCAATCCAATCTAATCT 60.017 38.462 0.00 0.00 0.00 2.40
190 210 2.689983 GGCGAAACATCCAATCCAATCT 59.310 45.455 0.00 0.00 0.00 2.40
204 224 0.038618 AATTTCTTGGCGGGCGAAAC 60.039 50.000 6.74 0.00 30.39 2.78
208 234 0.179148 GGTAAATTTCTTGGCGGGCG 60.179 55.000 0.00 0.00 0.00 6.13
231 257 8.267894 ACTAGTAAACCAAGGATCTACGTAGTA 58.732 37.037 21.53 9.50 45.11 1.82
234 260 8.267894 ACTACTAGTAAACCAAGGATCTACGTA 58.732 37.037 3.76 0.00 0.00 3.57
235 261 7.115414 ACTACTAGTAAACCAAGGATCTACGT 58.885 38.462 3.76 0.00 0.00 3.57
236 262 7.565323 ACTACTAGTAAACCAAGGATCTACG 57.435 40.000 3.76 0.00 0.00 3.51
289 315 3.890756 AGACAATGATGGAGTGCAAAACA 59.109 39.130 0.00 0.00 0.00 2.83
295 321 4.510038 ACAAAAGACAATGATGGAGTGC 57.490 40.909 0.00 0.00 0.00 4.40
310 336 4.611581 GCTGAACGAGCTAGGAAACAAAAG 60.612 45.833 0.00 0.00 45.21 2.27
338 368 4.448395 CGTGGTAGAATCTACTAGACTCCG 59.552 50.000 18.64 9.29 0.00 4.63
361 394 3.551485 GCAACATGCCATTTTTACCGATC 59.449 43.478 0.00 0.00 37.42 3.69
382 415 0.109132 CTTTTGCCCGTTCCATCAGC 60.109 55.000 0.00 0.00 0.00 4.26
400 433 1.617839 CTTCCTCCTCCCTTGGCCT 60.618 63.158 3.32 0.00 0.00 5.19
403 436 1.301293 GTGCTTCCTCCTCCCTTGG 59.699 63.158 0.00 0.00 0.00 3.61
404 437 1.078848 CGTGCTTCCTCCTCCCTTG 60.079 63.158 0.00 0.00 0.00 3.61
405 438 2.960688 GCGTGCTTCCTCCTCCCTT 61.961 63.158 0.00 0.00 0.00 3.95
406 439 3.394836 GCGTGCTTCCTCCTCCCT 61.395 66.667 0.00 0.00 0.00 4.20
408 441 2.185608 GAGCGTGCTTCCTCCTCC 59.814 66.667 0.00 0.00 0.00 4.30
409 442 2.185608 GGAGCGTGCTTCCTCCTC 59.814 66.667 0.00 0.00 43.42 3.71
410 443 2.604686 TGGAGCGTGCTTCCTCCT 60.605 61.111 14.99 0.00 46.23 3.69
411 444 2.435059 GTGGAGCGTGCTTCCTCC 60.435 66.667 9.32 9.32 46.25 4.30
412 445 1.739562 CAGTGGAGCGTGCTTCCTC 60.740 63.158 0.00 1.76 0.00 3.71
413 446 1.548357 ATCAGTGGAGCGTGCTTCCT 61.548 55.000 0.00 0.00 0.00 3.36
414 447 1.078848 ATCAGTGGAGCGTGCTTCC 60.079 57.895 0.00 0.93 0.00 3.46
415 448 0.108424 AGATCAGTGGAGCGTGCTTC 60.108 55.000 0.00 0.00 33.76 3.86
416 449 1.134965 GTAGATCAGTGGAGCGTGCTT 60.135 52.381 0.00 0.00 33.76 3.91
417 450 0.457851 GTAGATCAGTGGAGCGTGCT 59.542 55.000 0.00 0.00 33.76 4.40
418 451 0.457851 AGTAGATCAGTGGAGCGTGC 59.542 55.000 0.00 0.00 33.76 5.34
419 452 1.066303 GGAGTAGATCAGTGGAGCGTG 59.934 57.143 0.00 0.00 33.76 5.34
420 453 1.394618 GGAGTAGATCAGTGGAGCGT 58.605 55.000 0.00 0.00 33.76 5.07
421 454 0.309302 CGGAGTAGATCAGTGGAGCG 59.691 60.000 0.00 0.00 33.76 5.03
422 455 0.031449 GCGGAGTAGATCAGTGGAGC 59.969 60.000 0.00 0.00 0.00 4.70
423 456 1.393603 TGCGGAGTAGATCAGTGGAG 58.606 55.000 0.00 0.00 0.00 3.86
424 457 1.751351 CTTGCGGAGTAGATCAGTGGA 59.249 52.381 0.00 0.00 0.00 4.02
425 458 1.202463 CCTTGCGGAGTAGATCAGTGG 60.202 57.143 0.00 0.00 0.00 4.00
426 459 1.751351 TCCTTGCGGAGTAGATCAGTG 59.249 52.381 0.00 0.00 33.30 3.66
427 460 2.145397 TCCTTGCGGAGTAGATCAGT 57.855 50.000 0.00 0.00 33.30 3.41
428 461 2.351253 CGATCCTTGCGGAGTAGATCAG 60.351 54.545 11.49 3.59 44.06 2.90
429 462 1.609072 CGATCCTTGCGGAGTAGATCA 59.391 52.381 11.49 0.00 44.06 2.92
430 463 1.880675 TCGATCCTTGCGGAGTAGATC 59.119 52.381 3.75 3.75 44.06 2.75
431 464 1.609555 GTCGATCCTTGCGGAGTAGAT 59.390 52.381 0.00 0.00 44.06 1.98
465 498 3.692101 ACATTGTCTTGTGTTTTGACCGA 59.308 39.130 0.00 0.00 0.00 4.69
466 499 4.027572 ACATTGTCTTGTGTTTTGACCG 57.972 40.909 0.00 0.00 0.00 4.79
467 500 4.803613 GGAACATTGTCTTGTGTTTTGACC 59.196 41.667 0.00 0.00 38.57 4.02
478 515 1.072331 AGCCTCGTGGAACATTGTCTT 59.928 47.619 7.92 0.00 44.52 3.01
489 526 2.831742 TAGCCCGTAGCCTCGTGG 60.832 66.667 0.00 0.00 45.47 4.94
688 726 2.202544 GGCTGCGTCTCGTCTCAG 60.203 66.667 0.00 0.00 0.00 3.35
797 835 1.228657 GGCTTATAAAGGGCGCGAGG 61.229 60.000 12.10 0.00 0.00 4.63
822 860 3.256960 AAGGTGTGTGGGGGCGAT 61.257 61.111 0.00 0.00 0.00 4.58
870 908 3.947834 AGAGTGTGAAAACTGAAACTGGG 59.052 43.478 0.00 0.00 0.00 4.45
917 960 0.601311 GTTTGTCTCGCAGCTGGAGT 60.601 55.000 23.28 0.00 33.26 3.85
921 964 0.788995 CTCAGTTTGTCTCGCAGCTG 59.211 55.000 10.11 10.11 35.05 4.24
955 1003 1.153249 GACGGATTGGGCGATGGAA 60.153 57.895 0.00 0.00 0.00 3.53
956 1004 2.028125 GAGACGGATTGGGCGATGGA 62.028 60.000 0.00 0.00 0.00 3.41
979 1027 4.430137 TCTAATCGCGTACACAAGAACT 57.570 40.909 5.77 0.00 0.00 3.01
980 1028 4.026804 CCATCTAATCGCGTACACAAGAAC 60.027 45.833 5.77 0.00 0.00 3.01
982 1030 3.490249 CCCATCTAATCGCGTACACAAGA 60.490 47.826 5.77 2.45 0.00 3.02
984 1032 2.482316 CCCCATCTAATCGCGTACACAA 60.482 50.000 5.77 0.00 0.00 3.33
985 1033 1.067974 CCCCATCTAATCGCGTACACA 59.932 52.381 5.77 0.00 0.00 3.72
986 1034 1.779569 CCCCATCTAATCGCGTACAC 58.220 55.000 5.77 0.00 0.00 2.90
1035 1085 2.359975 GTCCACGGCCCCTTCTTG 60.360 66.667 0.00 0.00 0.00 3.02
1075 1125 2.555199 GTGCTTCTTGATGTAGGCGAT 58.445 47.619 0.00 0.00 0.00 4.58
1124 1174 2.017559 GAGTCGCTTACCGGCATCCT 62.018 60.000 0.00 0.00 45.91 3.24
1126 1176 1.944676 CGAGTCGCTTACCGGCATC 60.945 63.158 0.00 0.00 45.91 3.91
1168 1218 1.153449 TGTGGGATCGATCGGTTGC 60.153 57.895 18.81 8.54 0.00 4.17
1201 1271 8.774586 GCAACACAACCGATTAATTATCTATCT 58.225 33.333 0.00 0.00 0.00 1.98
1202 1272 7.740346 CGCAACACAACCGATTAATTATCTATC 59.260 37.037 0.00 0.00 0.00 2.08
1203 1273 7.225931 ACGCAACACAACCGATTAATTATCTAT 59.774 33.333 0.00 0.00 0.00 1.98
1204 1274 6.535865 ACGCAACACAACCGATTAATTATCTA 59.464 34.615 0.00 0.00 0.00 1.98
1205 1275 5.353123 ACGCAACACAACCGATTAATTATCT 59.647 36.000 0.00 0.00 0.00 1.98
1206 1276 5.565695 ACGCAACACAACCGATTAATTATC 58.434 37.500 0.00 0.00 0.00 1.75
1207 1277 5.353123 AGACGCAACACAACCGATTAATTAT 59.647 36.000 0.00 0.00 0.00 1.28
1208 1278 4.691685 AGACGCAACACAACCGATTAATTA 59.308 37.500 0.00 0.00 0.00 1.40
1209 1279 3.500680 AGACGCAACACAACCGATTAATT 59.499 39.130 0.00 0.00 0.00 1.40
1210 1280 3.071479 AGACGCAACACAACCGATTAAT 58.929 40.909 0.00 0.00 0.00 1.40
1211 1281 2.222213 CAGACGCAACACAACCGATTAA 59.778 45.455 0.00 0.00 0.00 1.40
1212 1282 1.795872 CAGACGCAACACAACCGATTA 59.204 47.619 0.00 0.00 0.00 1.75
1213 1283 0.586319 CAGACGCAACACAACCGATT 59.414 50.000 0.00 0.00 0.00 3.34
1214 1284 0.531974 ACAGACGCAACACAACCGAT 60.532 50.000 0.00 0.00 0.00 4.18
1215 1285 1.153529 ACAGACGCAACACAACCGA 60.154 52.632 0.00 0.00 0.00 4.69
1216 1286 1.011242 CACAGACGCAACACAACCG 60.011 57.895 0.00 0.00 0.00 4.44
1217 1287 0.248054 CACACAGACGCAACACAACC 60.248 55.000 0.00 0.00 0.00 3.77
1218 1288 0.446222 ACACACAGACGCAACACAAC 59.554 50.000 0.00 0.00 0.00 3.32
1219 1289 0.445829 CACACACAGACGCAACACAA 59.554 50.000 0.00 0.00 0.00 3.33
1233 1303 1.447217 CTCCAGGTCTGCACACACA 59.553 57.895 0.00 0.00 0.00 3.72
1248 1318 4.821589 CTCTTCCCGCACCGCTCC 62.822 72.222 0.00 0.00 0.00 4.70
1353 1423 2.046023 TTGCCGAGGATGCTGTGG 60.046 61.111 0.00 0.00 0.00 4.17
1390 1460 9.529325 GTGAACTGAGTGCATATATAGTTGTTA 57.471 33.333 0.00 0.00 0.00 2.41
1391 1461 8.040727 TGTGAACTGAGTGCATATATAGTTGTT 58.959 33.333 0.00 0.00 0.00 2.83
1392 1462 7.555965 TGTGAACTGAGTGCATATATAGTTGT 58.444 34.615 0.00 0.00 0.00 3.32
1393 1463 8.599055 ATGTGAACTGAGTGCATATATAGTTG 57.401 34.615 0.37 0.00 0.00 3.16
1394 1464 8.424133 TGATGTGAACTGAGTGCATATATAGTT 58.576 33.333 2.50 0.00 0.00 2.24
1395 1465 7.955918 TGATGTGAACTGAGTGCATATATAGT 58.044 34.615 2.50 0.00 0.00 2.12
1396 1466 8.999220 ATGATGTGAACTGAGTGCATATATAG 57.001 34.615 2.50 0.00 0.00 1.31
1397 1467 9.428097 GAATGATGTGAACTGAGTGCATATATA 57.572 33.333 2.50 0.00 0.00 0.86
1398 1468 7.935210 TGAATGATGTGAACTGAGTGCATATAT 59.065 33.333 2.50 0.00 0.00 0.86
1399 1469 7.274447 TGAATGATGTGAACTGAGTGCATATA 58.726 34.615 2.50 0.00 0.00 0.86
1400 1470 6.117488 TGAATGATGTGAACTGAGTGCATAT 58.883 36.000 2.08 2.08 0.00 1.78
1401 1471 5.490159 TGAATGATGTGAACTGAGTGCATA 58.510 37.500 0.00 0.00 0.00 3.14
1402 1472 4.329392 TGAATGATGTGAACTGAGTGCAT 58.671 39.130 0.00 0.00 0.00 3.96
1403 1473 3.742385 TGAATGATGTGAACTGAGTGCA 58.258 40.909 0.00 0.00 0.00 4.57
1404 1474 4.214971 AGTTGAATGATGTGAACTGAGTGC 59.785 41.667 0.00 0.00 0.00 4.40
1405 1475 5.389202 CGAGTTGAATGATGTGAACTGAGTG 60.389 44.000 0.00 0.00 0.00 3.51
1411 1481 3.428870 ACGTCGAGTTGAATGATGTGAAC 59.571 43.478 0.00 0.00 31.01 3.18
1456 1573 7.063780 CCTGAGCAATCATGTAAAATCAAAACC 59.936 37.037 0.00 0.00 0.00 3.27
1457 1574 7.599998 ACCTGAGCAATCATGTAAAATCAAAAC 59.400 33.333 0.00 0.00 0.00 2.43
1468 1592 1.352017 TGACCACCTGAGCAATCATGT 59.648 47.619 0.00 0.00 0.00 3.21
1641 1765 3.078836 GTGGGGTAGTAGGCGGCA 61.079 66.667 13.08 0.00 0.00 5.69
1948 2072 1.215647 CGTAGTCAGAGGCCACCAC 59.784 63.158 5.01 0.00 0.00 4.16
1954 2078 2.496817 CTGCCCGTAGTCAGAGGC 59.503 66.667 0.00 0.00 45.96 4.70
2163 2290 2.551270 CTCGTGTTGGCGCAGAAC 59.449 61.111 10.83 12.28 0.00 3.01
2176 2303 1.933853 GAAGGCGTCAATATTGCTCGT 59.066 47.619 23.14 11.57 0.00 4.18
2265 2392 4.756135 TGGAACCCGTACTTGTATTTTCAC 59.244 41.667 0.00 0.00 0.00 3.18
2295 2423 3.765511 ACTTAGTTTCCACATGCATGCAT 59.234 39.130 27.46 27.46 37.08 3.96
2311 2440 5.357257 ACGTGATGAACTGTTCAACTTAGT 58.643 37.500 25.26 18.92 43.95 2.24
2315 2444 4.945246 AGTACGTGATGAACTGTTCAACT 58.055 39.130 25.26 19.19 43.95 3.16
2318 2447 4.614306 CGGTAGTACGTGATGAACTGTTCA 60.614 45.833 23.94 23.94 45.01 3.18
2334 2463 1.528824 CCCCTCTCGGTCGGTAGTA 59.471 63.158 0.00 0.00 0.00 1.82
2335 2464 2.274760 CCCCTCTCGGTCGGTAGT 59.725 66.667 0.00 0.00 0.00 2.73
2336 2465 2.518825 CCCCCTCTCGGTCGGTAG 60.519 72.222 0.00 0.00 0.00 3.18
2347 2476 1.259840 ATGCATGTGTTTGCCCCCTC 61.260 55.000 0.00 0.00 42.06 4.30
2358 2487 3.362304 CGTACGTGATCATCATGCATGTG 60.362 47.826 25.43 21.04 36.89 3.21
2359 2488 2.796593 CGTACGTGATCATCATGCATGT 59.203 45.455 25.43 10.91 36.89 3.21
2360 2489 3.052036 TCGTACGTGATCATCATGCATG 58.948 45.455 21.07 21.07 36.89 4.06
2361 2490 3.004734 TCTCGTACGTGATCATCATGCAT 59.995 43.478 16.05 0.00 36.89 3.96
2362 2491 2.357637 TCTCGTACGTGATCATCATGCA 59.642 45.455 16.05 0.00 36.89 3.96
2363 2492 2.976509 CTCTCGTACGTGATCATCATGC 59.023 50.000 19.21 0.00 36.89 4.06
2364 2493 2.976509 GCTCTCGTACGTGATCATCATG 59.023 50.000 19.21 5.22 39.24 3.07
2365 2494 2.030717 GGCTCTCGTACGTGATCATCAT 60.031 50.000 19.21 0.00 0.00 2.45
2366 2495 1.333931 GGCTCTCGTACGTGATCATCA 59.666 52.381 19.21 0.00 0.00 3.07
2367 2496 1.660614 CGGCTCTCGTACGTGATCATC 60.661 57.143 19.21 9.58 0.00 2.92
2368 2497 0.308068 CGGCTCTCGTACGTGATCAT 59.692 55.000 19.21 0.00 0.00 2.45
2369 2498 1.719709 CGGCTCTCGTACGTGATCA 59.280 57.895 19.21 0.00 0.00 2.92
2370 2499 4.591852 CGGCTCTCGTACGTGATC 57.408 61.111 19.21 15.21 0.00 2.92
2455 2588 8.788806 TCGAAATAAGAATAACAGGAAAAGCAA 58.211 29.630 0.00 0.00 0.00 3.91
2568 2701 2.706339 ATGATGCAAGTGAGAGGGAC 57.294 50.000 0.00 0.00 0.00 4.46
2623 2756 6.207221 ACAAGAACAAACAGACATATGATGCA 59.793 34.615 10.38 0.00 0.00 3.96
2624 2757 6.615088 ACAAGAACAAACAGACATATGATGC 58.385 36.000 10.38 0.00 0.00 3.91
2625 2758 8.291740 TGAACAAGAACAAACAGACATATGATG 58.708 33.333 10.38 10.15 0.00 3.07
2626 2759 8.394971 TGAACAAGAACAAACAGACATATGAT 57.605 30.769 10.38 0.00 0.00 2.45
2628 2761 9.121517 GAATGAACAAGAACAAACAGACATATG 57.878 33.333 0.00 0.00 0.00 1.78
2629 2762 8.017373 CGAATGAACAAGAACAAACAGACATAT 58.983 33.333 0.00 0.00 0.00 1.78
2630 2763 7.225734 TCGAATGAACAAGAACAAACAGACATA 59.774 33.333 0.00 0.00 0.00 2.29
2631 2764 6.038161 TCGAATGAACAAGAACAAACAGACAT 59.962 34.615 0.00 0.00 0.00 3.06
2731 2886 6.144845 TCTCCCTCCATTTGATTTCTTCTT 57.855 37.500 0.00 0.00 0.00 2.52
2745 2900 3.977999 TCTAGTTGGTTTTTCTCCCTCCA 59.022 43.478 0.00 0.00 0.00 3.86
2825 2980 6.070424 ACTCCAGTCTATTTTCCCAACGATTA 60.070 38.462 0.00 0.00 0.00 1.75
2895 3051 1.012486 GGGTAACTGTTGGTCGCTCG 61.012 60.000 2.69 0.00 0.00 5.03
2918 3074 7.106439 ACAGAAAAACAAATACATGTGGTCA 57.894 32.000 9.11 0.00 32.81 4.02
2983 3141 8.635765 AGGAATGTAAACTTTGATGAAGCTTA 57.364 30.769 0.00 0.00 39.04 3.09
3080 3242 1.002366 CATGCAGCCTTGTACGAGTC 58.998 55.000 9.32 0.00 0.00 3.36
3118 3283 2.158682 ACACTACACACATTGGCCTTGA 60.159 45.455 3.32 0.00 0.00 3.02
3147 3312 7.609918 ACATACATTGAGTTGCTTTGGTATGTA 59.390 33.333 11.17 0.00 44.66 2.29
3159 3324 9.874215 CTAAGAATGCATACATACATTGAGTTG 57.126 33.333 0.00 0.00 36.65 3.16
3173 3338 6.092122 GCCATGCGTATAACTAAGAATGCATA 59.908 38.462 0.00 0.00 41.41 3.14
3193 3358 6.092122 ACGTACGGAAATAATGATATGCCATG 59.908 38.462 21.06 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.