Multiple sequence alignment - TraesCS3A01G374400

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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 TraesCS3A01G374400 chr3A 100.000 3271 0 0 1 3271 623940755 623944025 0.000000e+00 6041
1 TraesCS3A01G374400 chr3A 96.000 125 4 1 1569 1692 105556781 105556905 5.530000e-48 202
2 TraesCS3A01G374400 chr3B 90.768 2903 199 27 1 2889 642093001 642095848 0.000000e+00 3812
3 TraesCS3A01G374400 chr3B 93.041 388 23 3 2883 3268 642097371 642097756 6.130000e-157 564
4 TraesCS3A01G374400 chr7B 98.798 499 6 0 1 499 474799783 474800281 0.000000e+00 889
5 TraesCS3A01G374400 chr7B 96.000 125 4 1 1569 1692 662754859 662754983 5.530000e-48 202
6 TraesCS3A01G374400 chr6B 78.563 849 151 19 1693 2514 5714692 5713848 6.210000e-147 531
7 TraesCS3A01G374400 chr6B 83.636 495 71 5 1 489 425825219 425825709 1.070000e-124 457
8 TraesCS3A01G374400 chr6B 77.745 674 129 15 1693 2360 15106641 15107299 8.510000e-106 394
9 TraesCS3A01G374400 chr6B 77.858 551 105 13 1031 1571 5715233 5714690 3.150000e-85 326
10 TraesCS3A01G374400 chr6D 80.375 693 124 11 1693 2380 1539251 1538566 1.740000e-142 516
11 TraesCS3A01G374400 chr6D 78.674 694 122 19 1695 2379 8141151 8141827 3.870000e-119 438
12 TraesCS3A01G374400 chr6D 79.444 540 97 12 1031 1560 1539795 1539260 1.430000e-98 370
13 TraesCS3A01G374400 chr3D 82.941 510 66 10 1 493 550642259 550642764 1.080000e-119 440
14 TraesCS3A01G374400 chr1B 82.806 506 63 11 1 493 356564353 356564847 6.480000e-117 431
15 TraesCS3A01G374400 chr1B 96.000 125 4 1 1569 1692 347445925 347446049 5.530000e-48 202
16 TraesCS3A01G374400 chr1B 96.000 125 4 1 1569 1692 633717147 633717023 5.530000e-48 202
17 TraesCS3A01G374400 chr6A 78.417 695 125 19 1695 2380 8609652 8610330 2.330000e-116 429
18 TraesCS3A01G374400 chr6A 82.008 478 77 5 22 493 534988111 534987637 6.580000e-107 398
19 TraesCS3A01G374400 chr6A 80.664 512 74 15 1 494 183925177 183925681 1.110000e-99 374
20 TraesCS3A01G374400 chr6A 77.488 613 107 23 971 1565 8387936 8388535 4.040000e-89 339
21 TraesCS3A01G374400 chr6A 79.018 448 81 13 1888 2325 8388764 8389208 8.880000e-76 294
22 TraesCS3A01G374400 chr6A 79.515 371 67 7 998 1367 286331 286693 4.190000e-64 255
23 TraesCS3A01G374400 chr5A 76.339 896 157 31 1693 2548 129750140 129751020 2.330000e-116 429
24 TraesCS3A01G374400 chr5A 81.312 503 80 8 1 496 648364699 648364204 2.370000e-106 396
25 TraesCS3A01G374400 chr2D 82.697 445 66 6 55 493 122069937 122069498 5.120000e-103 385
26 TraesCS3A01G374400 chr7D 78.584 551 103 11 1031 1571 558888265 558887720 1.870000e-92 350
27 TraesCS3A01G374400 chr7D 83.851 322 48 4 1706 2026 558887712 558887394 1.470000e-78 303
28 TraesCS3A01G374400 chr7D 79.275 386 59 13 975 1360 7453855 7454219 1.950000e-62 250
29 TraesCS3A01G374400 chr7A 80.155 388 65 10 975 1362 8381230 8381605 2.490000e-71 279
30 TraesCS3A01G374400 chr4A 79.231 390 67 9 976 1363 732778917 732779294 3.240000e-65 259
31 TraesCS3A01G374400 chr5D 96.000 125 4 1 1569 1692 6253100 6253224 5.530000e-48 202
32 TraesCS3A01G374400 chr5D 96.000 125 4 1 1569 1692 299972332 299972456 5.530000e-48 202
33 TraesCS3A01G374400 chr5D 96.000 125 4 1 1569 1692 503313678 503313554 5.530000e-48 202
34 TraesCS3A01G374400 chr5B 96.000 125 4 1 1569 1692 57514949 57515073 5.530000e-48 202


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 TraesCS3A01G374400 chr3A 623940755 623944025 3270 False 6041.0 6041 100.0000 1 3271 1 chr3A.!!$F2 3270
1 TraesCS3A01G374400 chr3B 642093001 642097756 4755 False 2188.0 3812 91.9045 1 3268 2 chr3B.!!$F1 3267
2 TraesCS3A01G374400 chr6B 5713848 5715233 1385 True 428.5 531 78.2105 1031 2514 2 chr6B.!!$R1 1483
3 TraesCS3A01G374400 chr6B 15106641 15107299 658 False 394.0 394 77.7450 1693 2360 1 chr6B.!!$F1 667
4 TraesCS3A01G374400 chr6D 1538566 1539795 1229 True 443.0 516 79.9095 1031 2380 2 chr6D.!!$R1 1349
5 TraesCS3A01G374400 chr6D 8141151 8141827 676 False 438.0 438 78.6740 1695 2379 1 chr6D.!!$F1 684
6 TraesCS3A01G374400 chr3D 550642259 550642764 505 False 440.0 440 82.9410 1 493 1 chr3D.!!$F1 492
7 TraesCS3A01G374400 chr6A 8609652 8610330 678 False 429.0 429 78.4170 1695 2380 1 chr6A.!!$F2 685
8 TraesCS3A01G374400 chr6A 183925177 183925681 504 False 374.0 374 80.6640 1 494 1 chr6A.!!$F3 493
9 TraesCS3A01G374400 chr6A 8387936 8389208 1272 False 316.5 339 78.2530 971 2325 2 chr6A.!!$F4 1354
10 TraesCS3A01G374400 chr5A 129750140 129751020 880 False 429.0 429 76.3390 1693 2548 1 chr5A.!!$F1 855
11 TraesCS3A01G374400 chr7D 558887394 558888265 871 True 326.5 350 81.2175 1031 2026 2 chr7D.!!$R1 995

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
92 93 0.099968 TTACTCAGCGCGCGTAAGAT 59.900 50.0 32.35 16.76 43.02 2.40 F
210 212 0.178947 CTGCCCTTACCCACCCAAAA 60.179 55.0 0.00 0.00 0.00 2.44 F
268 274 0.252197 AAAGCCCTAACCTAGCCACG 59.748 55.0 0.00 0.00 0.00 4.94 F
959 984 0.460311 CTCGCTAAGGGTTCATCGGT 59.540 55.0 0.00 0.00 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1007 1032 0.679505 CTTCTTGGTGTCTCCCGTGA 59.320 55.0 0.00 0.00 34.77 4.35 R
1250 1275 0.869880 CGCGGTATCAGATGCAACGA 60.870 55.0 0.00 0.00 0.00 3.85 R
1619 1653 0.938008 GCTCGCCTTCTTATTTCCCG 59.062 55.0 0.00 0.00 0.00 5.14 R
2832 2947 0.037590 TAGGGCACGGTGCTTCAATT 59.962 50.0 29.92 13.11 44.28 2.32 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
30 31 1.203137 TCTATCAGGGGACGGGTATGG 60.203 57.143 0.00 0.00 0.00 2.74
32 33 2.265890 ATCAGGGGACGGGTATGGGT 62.266 60.000 0.00 0.00 0.00 4.51
33 34 1.999002 CAGGGGACGGGTATGGGTT 60.999 63.158 0.00 0.00 0.00 4.11
46 47 4.470602 GGTATGGGTTAGCTTTAATGCCT 58.529 43.478 9.56 1.13 0.00 4.75
57 58 0.181824 TTAATGCCTACGGGGAAGCC 59.818 55.000 0.75 0.00 36.28 4.35
61 62 3.396570 CCTACGGGGAAGCCGGTT 61.397 66.667 1.90 0.00 37.23 4.44
86 87 0.870307 AATACCTTACTCAGCGCGCG 60.870 55.000 28.44 28.44 0.00 6.86
87 88 2.001361 ATACCTTACTCAGCGCGCGT 62.001 55.000 32.35 20.17 0.00 6.01
88 89 1.368345 TACCTTACTCAGCGCGCGTA 61.368 55.000 32.35 19.03 0.00 4.42
90 91 1.472276 CCTTACTCAGCGCGCGTAAG 61.472 60.000 32.55 32.55 39.65 2.34
91 92 0.522705 CTTACTCAGCGCGCGTAAGA 60.523 55.000 34.44 25.82 41.45 2.10
92 93 0.099968 TTACTCAGCGCGCGTAAGAT 59.900 50.000 32.35 16.76 43.02 2.40
93 94 0.591488 TACTCAGCGCGCGTAAGATG 60.591 55.000 32.35 20.21 43.02 2.90
192 194 5.968676 TTAGTAGACCCCATGTAATTGCT 57.031 39.130 0.00 0.00 0.00 3.91
210 212 0.178947 CTGCCCTTACCCACCCAAAA 60.179 55.000 0.00 0.00 0.00 2.44
217 219 3.572642 CTTACCCACCCAAAACTCCTTT 58.427 45.455 0.00 0.00 0.00 3.11
233 235 2.925653 TCCTTTCATCCCATCCCTTTGA 59.074 45.455 0.00 0.00 0.00 2.69
235 237 3.564133 CCTTTCATCCCATCCCTTTGACA 60.564 47.826 0.00 0.00 0.00 3.58
268 274 0.252197 AAAGCCCTAACCTAGCCACG 59.748 55.000 0.00 0.00 0.00 4.94
318 324 9.830975 TGCTATGTTTTCTACTGAAATGCTATA 57.169 29.630 0.00 0.00 41.24 1.31
338 344 6.868339 GCTATAAAAGGTTGTTGTTGATTGCT 59.132 34.615 0.00 0.00 0.00 3.91
351 357 4.832266 TGTTGATTGCTTGTATGGGTTTCT 59.168 37.500 0.00 0.00 0.00 2.52
402 414 6.133356 GGTGGGGACAGGAATATTTTTATCA 58.867 40.000 0.00 0.00 44.46 2.15
408 420 7.201821 GGGACAGGAATATTTTTATCACCACAG 60.202 40.741 0.00 0.00 0.00 3.66
412 424 7.279981 CAGGAATATTTTTATCACCACAGACGA 59.720 37.037 0.00 0.00 0.00 4.20
421 433 1.144057 CCACAGACGAGTATGGGGC 59.856 63.158 6.19 0.00 38.66 5.80
442 454 2.367202 GGGACGGGCATGAGAAGGA 61.367 63.158 0.00 0.00 0.00 3.36
504 526 3.275143 CCATTGCCAGTGTTATCGGTAA 58.725 45.455 0.00 0.00 0.00 2.85
505 527 3.064820 CCATTGCCAGTGTTATCGGTAAC 59.935 47.826 11.75 11.75 40.48 2.50
525 547 1.417890 CACACTGTCCTCCTCAAGGTT 59.582 52.381 0.00 0.00 46.32 3.50
528 550 2.127708 ACTGTCCTCCTCAAGGTTTGT 58.872 47.619 0.00 0.00 46.32 2.83
576 598 9.155975 ACTCATACATCATAGTCACAAGAAAAC 57.844 33.333 0.00 0.00 0.00 2.43
582 604 6.072112 TCATAGTCACAAGAAAACCTTTGC 57.928 37.500 0.00 0.00 31.42 3.68
585 607 3.706086 AGTCACAAGAAAACCTTTGCCAT 59.294 39.130 0.00 0.00 31.42 4.40
603 625 3.864921 GCCATGTAGACCGGCTTATAAGG 60.865 52.174 14.28 0.15 42.78 2.69
604 626 3.323979 CCATGTAGACCGGCTTATAAGGT 59.676 47.826 14.28 4.65 41.63 3.50
665 688 5.178067 CCAAAGATGCCAAAGTTGTTTCATC 59.822 40.000 8.75 8.75 32.57 2.92
707 730 3.936902 TTTTTGGTCTCGTTGAACTCG 57.063 42.857 0.00 0.00 32.49 4.18
708 731 2.589798 TTTGGTCTCGTTGAACTCGT 57.410 45.000 0.00 0.00 32.49 4.18
709 732 3.713858 TTTGGTCTCGTTGAACTCGTA 57.286 42.857 0.00 0.00 32.49 3.43
710 733 2.693797 TGGTCTCGTTGAACTCGTAC 57.306 50.000 0.00 0.00 32.49 3.67
711 734 1.267806 TGGTCTCGTTGAACTCGTACC 59.732 52.381 0.00 0.00 36.65 3.34
712 735 1.267806 GGTCTCGTTGAACTCGTACCA 59.732 52.381 0.00 0.00 36.38 3.25
713 736 2.287788 GGTCTCGTTGAACTCGTACCAA 60.288 50.000 0.00 0.00 36.38 3.67
714 737 3.374745 GTCTCGTTGAACTCGTACCAAA 58.625 45.455 0.00 0.00 0.00 3.28
715 738 3.985925 GTCTCGTTGAACTCGTACCAAAT 59.014 43.478 0.00 0.00 0.00 2.32
716 739 4.446719 GTCTCGTTGAACTCGTACCAAATT 59.553 41.667 0.00 0.00 0.00 1.82
758 781 5.482163 CCAAATTTGGTCTGGTTTGGTAT 57.518 39.130 26.34 0.00 43.40 2.73
769 792 6.295632 GGTCTGGTTTGGTATTATTTGGCTTT 60.296 38.462 0.00 0.00 0.00 3.51
817 841 2.296945 TAGCCATCCACCCATTGCCC 62.297 60.000 0.00 0.00 0.00 5.36
822 846 1.814292 ATCCACCCATTGCCCAACCT 61.814 55.000 0.00 0.00 0.00 3.50
910 935 4.083324 CGCAACAAAGCTTCCATCTTCTTA 60.083 41.667 0.00 0.00 0.00 2.10
915 940 5.355350 ACAAAGCTTCCATCTTCTTATTCCG 59.645 40.000 0.00 0.00 0.00 4.30
947 972 2.537143 AGAGTTTCCCCTTCTCGCTAA 58.463 47.619 0.00 0.00 33.96 3.09
956 981 2.827652 CCTTCTCGCTAAGGGTTCATC 58.172 52.381 7.52 0.00 42.08 2.92
959 984 0.460311 CTCGCTAAGGGTTCATCGGT 59.540 55.000 0.00 0.00 0.00 4.69
965 990 1.562672 AAGGGTTCATCGGTCCCCAG 61.563 60.000 0.00 0.00 41.95 4.45
1022 1047 2.863346 CGGTCACGGGAGACACCAA 61.863 63.158 0.00 0.00 40.29 3.67
1023 1048 1.004918 GGTCACGGGAGACACCAAG 60.005 63.158 0.00 0.00 40.29 3.61
1059 1084 3.776969 TCATGCTAAAGACCTCAGATGGT 59.223 43.478 0.00 0.00 44.10 3.55
1143 1168 3.470567 GAGTGCGCCGACAACGAG 61.471 66.667 4.18 0.00 42.66 4.18
1273 1298 1.289066 GCATCTGATACCGCGGCTA 59.711 57.895 28.58 17.32 0.00 3.93
1308 1333 2.192263 GAGGACCTCAAGAACTGGGAT 58.808 52.381 17.10 0.00 0.00 3.85
1310 1335 1.630878 GGACCTCAAGAACTGGGATGT 59.369 52.381 0.00 0.00 0.00 3.06
1316 1341 4.142049 CCTCAAGAACTGGGATGTAGAGTC 60.142 50.000 0.00 0.00 0.00 3.36
1318 1343 2.379972 AGAACTGGGATGTAGAGTCCG 58.620 52.381 0.00 0.00 36.58 4.79
1379 1404 7.255836 CCTGGTATGATATCCTTTAGTTCGACA 60.256 40.741 0.00 0.00 0.00 4.35
1471 1504 3.206150 CGTCTTGCATATTAGCTTGGGT 58.794 45.455 0.00 0.00 34.99 4.51
1511 1544 7.295322 TCATCAAGGTAGATTCTCGATTCAT 57.705 36.000 0.00 0.00 0.00 2.57
1619 1653 5.494390 TCCCACTTTCCTAAACTAAGGAC 57.506 43.478 0.00 0.00 45.49 3.85
1640 1674 2.576615 GGGAAATAAGAAGGCGAGCAT 58.423 47.619 0.00 0.00 0.00 3.79
2014 2090 4.178545 ACACATCTTAATGCAAGGCAAC 57.821 40.909 0.00 0.00 43.62 4.17
2122 2200 3.124297 GCATGCTATCTTAACATCGAGGC 59.876 47.826 11.37 0.00 0.00 4.70
2186 2264 2.433239 GGGCAAAACTACGGAGGAGATA 59.567 50.000 0.00 0.00 0.00 1.98
2284 2372 2.290464 TGAGTAGAGGAGCGTCTAAGC 58.710 52.381 1.87 0.00 30.70 3.09
2306 2394 4.201628 GCTACACTGAATGAACGCTTACTG 60.202 45.833 0.00 0.00 0.00 2.74
2486 2601 5.877012 CACTCACCTAAAGCACTCATACAAT 59.123 40.000 0.00 0.00 0.00 2.71
2507 2622 8.302515 ACAATCAATATTTTCTCTTGAGCCAT 57.697 30.769 0.00 0.00 32.82 4.40
2540 2655 6.828273 TCATAATGTAGTTGCTTAACATGCCT 59.172 34.615 0.00 0.00 34.20 4.75
2555 2670 2.526304 TGCCTATATGCTCAACCGTC 57.474 50.000 1.58 0.00 0.00 4.79
2568 2683 1.396996 CAACCGTCCGATCAACCATTC 59.603 52.381 0.00 0.00 0.00 2.67
2573 2688 1.089481 TCCGATCAACCATTCAGCGC 61.089 55.000 0.00 0.00 0.00 5.92
2582 2697 2.104331 ATTCAGCGCGACCTACCG 59.896 61.111 12.10 0.00 0.00 4.02
2612 2727 2.184020 TAGGCCATGTTGCGCTCACT 62.184 55.000 9.73 4.34 0.00 3.41
2616 2731 0.806868 CCATGTTGCGCTCACTGATT 59.193 50.000 9.73 0.00 0.00 2.57
2627 2742 2.417933 GCTCACTGATTTGTGCTAGTGG 59.582 50.000 0.00 0.00 40.59 4.00
2628 2743 3.668447 CTCACTGATTTGTGCTAGTGGT 58.332 45.455 0.00 0.00 40.59 4.16
2651 2766 1.003355 CGTCCAGCCACAGGTGAAT 60.003 57.895 0.00 0.00 44.53 2.57
2652 2767 1.300971 CGTCCAGCCACAGGTGAATG 61.301 60.000 0.00 0.00 44.53 2.67
2657 2772 1.682854 CAGCCACAGGTGAATGTTTGT 59.317 47.619 0.00 0.00 44.53 2.83
2727 2842 0.035056 CCAAGCAGGTCGAAATCCCT 60.035 55.000 0.00 0.00 0.00 4.20
2832 2947 0.178938 TTGGATGCAGGGGAAAAGCA 60.179 50.000 0.00 0.00 43.14 3.91
2842 2957 2.037641 AGGGGAAAAGCAATTGAAGCAC 59.962 45.455 10.34 0.00 0.00 4.40
2861 2976 2.883828 CGTGCCCTAGCCCCCTATG 61.884 68.421 0.00 0.00 38.69 2.23
2909 4554 2.885113 CATCGGTGCTCGGTCTGA 59.115 61.111 0.00 0.00 39.77 3.27
2944 4591 1.362584 TGGAGGGAGAGATGGTGAGAA 59.637 52.381 0.00 0.00 0.00 2.87
2954 4601 5.271598 AGAGATGGTGAGAAAGAGATGAGT 58.728 41.667 0.00 0.00 0.00 3.41
2980 4627 0.889186 GAAGACAATGTGGGTGCCGT 60.889 55.000 0.00 0.00 0.00 5.68
3022 4669 1.537889 ATGACACGGGAGGGGTTGA 60.538 57.895 0.00 0.00 37.82 3.18
3025 4672 4.388499 CACGGGAGGGGTTGACGG 62.388 72.222 0.00 0.00 0.00 4.79
3050 4697 0.663269 GTGTCACTCGTCGATGCACA 60.663 55.000 0.00 0.00 0.00 4.57
3062 4709 4.205181 CGTCGATGCACACTCTTGTATTAG 59.795 45.833 0.00 0.00 33.30 1.73
3067 4714 1.588404 CACACTCTTGTATTAGCGCGG 59.412 52.381 8.83 0.00 33.30 6.46
3076 4723 2.937149 TGTATTAGCGCGGTTATTGCAA 59.063 40.909 19.09 0.00 0.00 4.08
3139 4786 5.238650 ACTTACTTGGGACTTTGACGATTTG 59.761 40.000 0.00 0.00 0.00 2.32
3151 4798 2.224426 TGACGATTTGCCACTGGTTAGT 60.224 45.455 0.00 0.00 37.75 2.24
3197 4844 9.131791 ACTTCTTAGGTGCTCTTTTTCAATAAA 57.868 29.630 0.00 0.00 0.00 1.40
3198 4845 9.965824 CTTCTTAGGTGCTCTTTTTCAATAAAA 57.034 29.630 0.00 0.00 32.75 1.52
3269 4916 9.503427 GCATAAAAATAGTGGACAATAACACTC 57.497 33.333 0.03 0.00 44.08 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 2.582226 CCATCTTACGCGCGCTGA 60.582 61.111 32.58 24.64 0.00 4.26
86 87 1.355720 CCATCCCCATCCCCATCTTAC 59.644 57.143 0.00 0.00 0.00 2.34
87 88 1.759101 CCATCCCCATCCCCATCTTA 58.241 55.000 0.00 0.00 0.00 2.10
88 89 1.076095 CCCATCCCCATCCCCATCTT 61.076 60.000 0.00 0.00 0.00 2.40
90 91 0.852683 ATCCCATCCCCATCCCCATC 60.853 60.000 0.00 0.00 0.00 3.51
91 92 0.507104 TATCCCATCCCCATCCCCAT 59.493 55.000 0.00 0.00 0.00 4.00
92 93 0.178834 CTATCCCATCCCCATCCCCA 60.179 60.000 0.00 0.00 0.00 4.96
93 94 1.575447 GCTATCCCATCCCCATCCCC 61.575 65.000 0.00 0.00 0.00 4.81
192 194 0.470268 GTTTTGGGTGGGTAAGGGCA 60.470 55.000 0.00 0.00 0.00 5.36
210 212 2.293598 AGGGATGGGATGAAAGGAGT 57.706 50.000 0.00 0.00 0.00 3.85
217 219 3.824001 TTTGTCAAAGGGATGGGATGA 57.176 42.857 0.00 0.00 0.00 2.92
245 247 2.026262 TGGCTAGGTTAGGGCTTTCTTG 60.026 50.000 0.00 0.00 0.00 3.02
252 254 1.143401 GTCGTGGCTAGGTTAGGGC 59.857 63.158 0.00 0.00 0.00 5.19
318 324 5.244755 ACAAGCAATCAACAACAACCTTTT 58.755 33.333 0.00 0.00 0.00 2.27
338 344 2.024464 CCCCATGGAGAAACCCATACAA 60.024 50.000 15.22 0.00 44.69 2.41
379 385 6.040504 GGTGATAAAAATATTCCTGTCCCCAC 59.959 42.308 0.00 0.00 0.00 4.61
386 398 7.279981 TCGTCTGTGGTGATAAAAATATTCCTG 59.720 37.037 0.00 0.00 0.00 3.86
402 414 1.614241 GCCCCATACTCGTCTGTGGT 61.614 60.000 0.00 0.00 0.00 4.16
408 420 2.808206 CCCCAGCCCCATACTCGTC 61.808 68.421 0.00 0.00 0.00 4.20
412 424 2.768344 CGTCCCCAGCCCCATACT 60.768 66.667 0.00 0.00 0.00 2.12
421 433 2.599645 CTTCTCATGCCCGTCCCCAG 62.600 65.000 0.00 0.00 0.00 4.45
436 448 1.762460 ATCCCCGCGACATCCTTCT 60.762 57.895 8.23 0.00 0.00 2.85
442 454 3.550431 CTCCCATCCCCGCGACAT 61.550 66.667 8.23 0.00 0.00 3.06
542 564 9.860898 GTGACTATGATGTATGAGTGCAATATA 57.139 33.333 0.00 0.00 0.00 0.86
543 565 8.370182 TGTGACTATGATGTATGAGTGCAATAT 58.630 33.333 0.00 0.00 0.00 1.28
551 573 8.607459 GGTTTTCTTGTGACTATGATGTATGAG 58.393 37.037 0.00 0.00 0.00 2.90
561 583 4.892934 TGGCAAAGGTTTTCTTGTGACTAT 59.107 37.500 0.00 0.00 35.55 2.12
564 586 3.518634 TGGCAAAGGTTTTCTTGTGAC 57.481 42.857 0.00 0.00 35.55 3.67
576 598 2.780595 CCGGTCTACATGGCAAAGG 58.219 57.895 0.00 0.00 0.00 3.11
582 604 3.323979 ACCTTATAAGCCGGTCTACATGG 59.676 47.826 1.90 1.22 0.00 3.66
585 607 2.696707 CCACCTTATAAGCCGGTCTACA 59.303 50.000 1.90 0.00 0.00 2.74
616 638 2.279851 TGCTTCACCACCGTCACG 60.280 61.111 0.00 0.00 0.00 4.35
617 639 0.814010 AACTGCTTCACCACCGTCAC 60.814 55.000 0.00 0.00 0.00 3.67
618 640 0.531974 GAACTGCTTCACCACCGTCA 60.532 55.000 0.00 0.00 0.00 4.35
665 688 8.614994 AAAAACTCATATTTTCCTATTTCGCG 57.385 30.769 0.00 0.00 31.35 5.87
692 715 1.267806 TGGTACGAGTTCAACGAGACC 59.732 52.381 0.00 0.00 39.09 3.85
693 716 2.693797 TGGTACGAGTTCAACGAGAC 57.306 50.000 0.00 0.00 34.70 3.36
694 717 3.713858 TTTGGTACGAGTTCAACGAGA 57.286 42.857 0.00 0.00 34.70 4.04
695 718 4.985044 AATTTGGTACGAGTTCAACGAG 57.015 40.909 0.00 0.00 34.70 4.18
696 719 4.024725 CCAAATTTGGTACGAGTTCAACGA 60.025 41.667 26.34 0.00 43.43 3.85
697 720 4.215965 CCAAATTTGGTACGAGTTCAACG 58.784 43.478 26.34 0.00 43.43 4.10
710 733 7.207689 ACGAGTTCAACGAGACCAAATTTGG 62.208 44.000 31.42 31.42 42.73 3.28
711 734 4.211389 CGAGTTCAACGAGACCAAATTTG 58.789 43.478 11.40 11.40 0.00 2.32
712 735 3.875134 ACGAGTTCAACGAGACCAAATTT 59.125 39.130 0.00 0.00 34.70 1.82
713 736 3.463944 ACGAGTTCAACGAGACCAAATT 58.536 40.909 0.00 0.00 34.70 1.82
714 737 3.107642 ACGAGTTCAACGAGACCAAAT 57.892 42.857 0.00 0.00 34.70 2.32
715 738 2.589798 ACGAGTTCAACGAGACCAAA 57.410 45.000 0.00 0.00 34.70 3.28
716 739 2.287788 GGTACGAGTTCAACGAGACCAA 60.288 50.000 0.00 0.00 38.78 3.67
747 770 7.977789 AAAAAGCCAAATAATACCAAACCAG 57.022 32.000 0.00 0.00 0.00 4.00
769 792 5.191727 TCTATCATGCCTCCAAAGGAAAA 57.808 39.130 0.00 0.00 46.67 2.29
773 797 5.752036 TCTATCTATCATGCCTCCAAAGG 57.248 43.478 0.00 0.00 46.44 3.11
817 841 0.614415 TATTGGGGCAAGGCAGGTTG 60.614 55.000 0.00 0.00 0.00 3.77
822 846 0.328592 TTACGTATTGGGGCAAGGCA 59.671 50.000 0.00 0.00 0.00 4.75
915 940 3.952628 AAACTCTAGTGGCGGCGGC 62.953 63.158 27.76 27.76 38.90 6.53
965 990 4.696805 GGGTTGGGGTGGAAGGGC 62.697 72.222 0.00 0.00 0.00 5.19
977 1002 2.190578 GGATCCGAGCTGGGGTTG 59.809 66.667 15.52 0.00 38.76 3.77
1007 1032 0.679505 CTTCTTGGTGTCTCCCGTGA 59.320 55.000 0.00 0.00 34.77 4.35
1059 1084 2.493675 CTCCTCGACCTCAAACTCATCA 59.506 50.000 0.00 0.00 0.00 3.07
1098 1123 1.820906 CATGTGGCGGATGGTCAGG 60.821 63.158 0.00 0.00 0.00 3.86
1143 1168 1.684983 TCGACGTTGGGGATTAGGATC 59.315 52.381 2.20 0.00 0.00 3.36
1250 1275 0.869880 CGCGGTATCAGATGCAACGA 60.870 55.000 0.00 0.00 0.00 3.85
1273 1298 2.660064 CCTCTGCTAGGGTGGCGTT 61.660 63.158 0.00 0.00 42.32 4.84
1308 1333 2.281539 TGACCTTGACGGACTCTACA 57.718 50.000 0.00 0.00 36.31 2.74
1310 1335 1.891150 GGTTGACCTTGACGGACTCTA 59.109 52.381 0.00 0.00 36.31 2.43
1316 1341 1.666872 GTCGGGTTGACCTTGACGG 60.667 63.158 9.26 0.00 42.04 4.79
1430 1455 4.079253 ACGTGCAAACCCAATCTAGATTT 58.921 39.130 15.49 0.00 0.00 2.17
1471 1504 8.211030 ACCTTGATGATGATATGAGTATTCCA 57.789 34.615 0.00 0.00 0.00 3.53
1511 1544 9.472361 CCTAAACCTAATCTAATCGAATCGAAA 57.528 33.333 10.12 0.00 39.99 3.46
1549 1582 1.869767 GGACATCGCCAATAGAGCAAG 59.130 52.381 0.00 0.00 0.00 4.01
1595 1628 5.938710 GTCCTTAGTTTAGGAAAGTGGGAAG 59.061 44.000 0.00 0.00 45.62 3.46
1596 1629 5.511888 CGTCCTTAGTTTAGGAAAGTGGGAA 60.512 44.000 0.00 0.00 45.62 3.97
1598 1631 4.251268 CGTCCTTAGTTTAGGAAAGTGGG 58.749 47.826 0.00 0.00 45.62 4.61
1619 1653 0.938008 GCTCGCCTTCTTATTTCCCG 59.062 55.000 0.00 0.00 0.00 5.14
1667 1701 2.736670 CCCCATTCTAGGAAGGGTTG 57.263 55.000 10.54 0.00 39.76 3.77
1773 1809 4.426416 CCAGGTTATGCATGACAACAATG 58.574 43.478 21.65 13.62 0.00 2.82
2059 2135 4.955811 AGAACCACATAGTGTCACAGAA 57.044 40.909 5.62 0.00 0.00 3.02
2063 2139 5.163754 GGCAATAAGAACCACATAGTGTCAC 60.164 44.000 0.00 0.00 0.00 3.67
2122 2200 4.408921 TCTGGGATATTAGGTTCACCAGTG 59.591 45.833 0.00 0.00 43.34 3.66
2186 2264 2.254546 TCAGGTTGAACATCTTGCGT 57.745 45.000 0.00 0.00 0.00 5.24
2284 2372 4.923871 ACAGTAAGCGTTCATTCAGTGTAG 59.076 41.667 0.00 0.00 0.00 2.74
2286 2374 3.728845 ACAGTAAGCGTTCATTCAGTGT 58.271 40.909 0.00 0.00 0.00 3.55
2306 2394 5.947228 TCTCAAAGGTTGACATGATGAAC 57.053 39.130 0.00 0.00 35.46 3.18
2486 2601 7.394077 TCACAATGGCTCAAGAGAAAATATTGA 59.606 33.333 0.32 0.00 36.79 2.57
2536 2651 1.070134 GGACGGTTGAGCATATAGGCA 59.930 52.381 12.54 0.00 35.83 4.75
2540 2655 2.888414 TGATCGGACGGTTGAGCATATA 59.112 45.455 0.00 0.00 0.00 0.86
2555 2670 1.353103 GCGCTGAATGGTTGATCGG 59.647 57.895 0.00 0.00 0.00 4.18
2640 2755 2.687425 TGTCACAAACATTCACCTGTGG 59.313 45.455 0.00 0.00 39.69 4.17
2645 2760 4.218200 TGATCCATGTCACAAACATTCACC 59.782 41.667 0.00 0.00 46.73 4.02
2651 2766 5.360429 CCCAATATGATCCATGTCACAAACA 59.640 40.000 0.00 0.00 43.51 2.83
2652 2767 5.221303 CCCCAATATGATCCATGTCACAAAC 60.221 44.000 0.00 0.00 0.00 2.93
2657 2772 3.721050 TGACCCCAATATGATCCATGTCA 59.279 43.478 0.00 0.00 0.00 3.58
2666 2781 3.245229 ACTTGCAAGTGACCCCAATATGA 60.245 43.478 30.66 0.00 37.98 2.15
2673 2788 1.363807 GCAACTTGCAAGTGACCCC 59.636 57.895 31.73 14.59 44.26 4.95
2810 2925 2.678769 GCTTTTCCCCTGCATCCAAATG 60.679 50.000 0.00 0.00 35.87 2.32
2818 2933 1.714541 TCAATTGCTTTTCCCCTGCA 58.285 45.000 0.00 0.00 34.69 4.41
2820 2935 2.037511 TGCTTCAATTGCTTTTCCCCTG 59.962 45.455 0.00 0.00 0.00 4.45
2832 2947 0.037590 TAGGGCACGGTGCTTCAATT 59.962 50.000 29.92 13.11 44.28 2.32
2842 2957 4.872574 TAGGGGGCTAGGGCACGG 62.873 72.222 0.00 0.00 44.06 4.94
2903 4548 7.118496 TCCATTTCTCTATTCTCTTCAGACC 57.882 40.000 0.00 0.00 0.00 3.85
2909 4554 6.448202 TCTCCCTCCATTTCTCTATTCTCTT 58.552 40.000 0.00 0.00 0.00 2.85
2944 4591 5.083122 TGTCTTCCTCTCAACTCATCTCTT 58.917 41.667 0.00 0.00 0.00 2.85
2954 4601 2.711009 ACCCACATTGTCTTCCTCTCAA 59.289 45.455 0.00 0.00 0.00 3.02
2980 4627 4.155709 CCATACCTCTCTAGAAGCATCCA 58.844 47.826 0.00 0.00 0.00 3.41
3022 4669 0.391597 ACGAGTGACACATTTCCCGT 59.608 50.000 8.59 4.63 0.00 5.28
3025 4672 2.060326 TCGACGAGTGACACATTTCC 57.940 50.000 8.59 0.00 0.00 3.13
3050 4697 2.667473 AACCGCGCTAATACAAGAGT 57.333 45.000 5.56 0.00 0.00 3.24
3062 4709 2.152078 GCACTTGCAATAACCGCGC 61.152 57.895 0.00 0.00 41.59 6.86
3067 4714 6.836577 TTTTTGGTAAGCACTTGCAATAAC 57.163 33.333 0.00 0.00 45.16 1.89
3076 4723 1.623311 GGCCCATTTTTGGTAAGCACT 59.377 47.619 0.00 0.00 0.00 4.40
3139 4786 5.699097 TCAATTACAAACTAACCAGTGGC 57.301 39.130 9.78 0.00 34.36 5.01
3169 4816 5.437060 TGAAAAAGAGCACCTAAGAAGTGT 58.563 37.500 0.00 0.00 37.56 3.55
3170 4817 6.377327 TTGAAAAAGAGCACCTAAGAAGTG 57.623 37.500 0.00 0.00 38.30 3.16
3213 4860 8.465999 TGCATATTATCGAAAACATTTGAAGGT 58.534 29.630 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.