Multiple sequence alignment - TraesCS3B01G068000

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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 TraesCS3B01G068000 chr3B 100.000 3605 0 0 1 3605 40246586 40242982 0.000000e+00 6658
1 TraesCS3B01G068000 chr3D 94.127 1958 84 14 741 2678 23063817 23061871 0.000000e+00 2950
2 TraesCS3B01G068000 chr3D 93.608 704 35 5 1 697 23064514 23063814 0.000000e+00 1042
3 TraesCS3B01G068000 chr3A 91.417 2004 117 27 1 1982 32152776 32150806 0.000000e+00 2697
4 TraesCS3B01G068000 chr3A 93.814 582 31 5 2098 2678 32150592 32150015 0.000000e+00 870
5 TraesCS3B01G068000 chr3A 92.557 524 32 4 2678 3194 562985795 562985272 0.000000e+00 745
6 TraesCS3B01G068000 chr3A 94.258 418 23 1 3189 3605 375380906 375381323 3.930000e-179 638
7 TraesCS3B01G068000 chr1D 93.598 656 32 5 1 649 225396887 225397539 0.000000e+00 970
8 TraesCS3B01G068000 chr7A 98.269 520 6 2 2678 3194 11555010 11555529 0.000000e+00 907
9 TraesCS3B01G068000 chr7A 99.041 417 4 0 3189 3605 11555484 11555900 0.000000e+00 749
10 TraesCS3B01G068000 chr5A 97.710 524 8 3 2675 3194 473424147 473423624 0.000000e+00 898
11 TraesCS3B01G068000 chr5A 99.281 417 3 0 3189 3605 473423669 473423253 0.000000e+00 754
12 TraesCS3B01G068000 chr5A 94.019 418 23 2 3189 3605 685761585 685762001 1.830000e-177 632
13 TraesCS3B01G068000 chr4B 97.619 504 9 2 2687 3188 392652605 392653107 0.000000e+00 861
14 TraesCS3B01G068000 chr4B 98.801 417 5 0 3189 3605 392653069 392653485 0.000000e+00 743
15 TraesCS3B01G068000 chr7B 93.321 524 28 4 2678 3194 44362295 44362818 0.000000e+00 767
16 TraesCS3B01G068000 chr6A 93.077 520 30 3 2678 3191 561437811 561437292 0.000000e+00 756
17 TraesCS3B01G068000 chr6A 92.557 524 32 4 2678 3194 561616066 561616589 0.000000e+00 745
18 TraesCS3B01G068000 chr6A 94.737 418 18 2 3189 3605 561437333 561436919 0.000000e+00 647
19 TraesCS3B01G068000 chr6A 94.737 418 18 2 3189 3605 561616544 561616958 0.000000e+00 647
20 TraesCS3B01G068000 chr2B 91.620 537 33 7 2668 3194 586402151 586402685 0.000000e+00 732
21 TraesCS3B01G068000 chr2B 79.405 874 136 30 995 1848 491181323 491182172 8.680000e-161 577
22 TraesCS3B01G068000 chr1B 91.434 537 34 7 2668 3194 659060075 659059541 0.000000e+00 726
23 TraesCS3B01G068000 chr1B 94.019 418 24 1 3189 3605 10839253 10839670 1.830000e-177 632
24 TraesCS3B01G068000 chr2D 95.215 418 18 2 3189 3605 48329508 48329092 0.000000e+00 660
25 TraesCS3B01G068000 chr2D 79.725 873 135 28 995 1848 419040491 419041340 8.620000e-166 593
26 TraesCS3B01G068000 chr2A 83.390 590 80 14 995 1581 570785192 570784618 6.850000e-147 531
27 TraesCS3B01G068000 chr2A 86.331 139 19 0 1710 1848 570784481 570784343 6.230000e-33 152


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 TraesCS3B01G068000 chr3B 40242982 40246586 3604 True 6658.0 6658 100.0000 1 3605 1 chr3B.!!$R1 3604
1 TraesCS3B01G068000 chr3D 23061871 23064514 2643 True 1996.0 2950 93.8675 1 2678 2 chr3D.!!$R1 2677
2 TraesCS3B01G068000 chr3A 32150015 32152776 2761 True 1783.5 2697 92.6155 1 2678 2 chr3A.!!$R2 2677
3 TraesCS3B01G068000 chr3A 562985272 562985795 523 True 745.0 745 92.5570 2678 3194 1 chr3A.!!$R1 516
4 TraesCS3B01G068000 chr1D 225396887 225397539 652 False 970.0 970 93.5980 1 649 1 chr1D.!!$F1 648
5 TraesCS3B01G068000 chr7A 11555010 11555900 890 False 828.0 907 98.6550 2678 3605 2 chr7A.!!$F1 927
6 TraesCS3B01G068000 chr5A 473423253 473424147 894 True 826.0 898 98.4955 2675 3605 2 chr5A.!!$R1 930
7 TraesCS3B01G068000 chr4B 392652605 392653485 880 False 802.0 861 98.2100 2687 3605 2 chr4B.!!$F1 918
8 TraesCS3B01G068000 chr7B 44362295 44362818 523 False 767.0 767 93.3210 2678 3194 1 chr7B.!!$F1 516
9 TraesCS3B01G068000 chr6A 561436919 561437811 892 True 701.5 756 93.9070 2678 3605 2 chr6A.!!$R1 927
10 TraesCS3B01G068000 chr6A 561616066 561616958 892 False 696.0 745 93.6470 2678 3605 2 chr6A.!!$F1 927
11 TraesCS3B01G068000 chr2B 586402151 586402685 534 False 732.0 732 91.6200 2668 3194 1 chr2B.!!$F2 526
12 TraesCS3B01G068000 chr2B 491181323 491182172 849 False 577.0 577 79.4050 995 1848 1 chr2B.!!$F1 853
13 TraesCS3B01G068000 chr1B 659059541 659060075 534 True 726.0 726 91.4340 2668 3194 1 chr1B.!!$R1 526
14 TraesCS3B01G068000 chr2D 419040491 419041340 849 False 593.0 593 79.7250 995 1848 1 chr2D.!!$F1 853
15 TraesCS3B01G068000 chr2A 570784343 570785192 849 True 341.5 531 84.8605 995 1848 2 chr2A.!!$R1 853

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
634 642 0.034477 GGGTACTGATGGGTTGGTGG 60.034 60.0 0.00 0.00 0.00 4.61 F
1446 1457 0.950116 GGCATAGAGTTCCTGCATGC 59.050 55.0 11.82 11.82 40.96 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 1604 0.313672 TGAAATCCACGGCAAGCAAC 59.686 50.0 0.0 0.0 0.0 4.17 R
3167 3331 0.250727 TCTTTCCTTCCTGCCAACGG 60.251 55.0 0.0 0.0 0.0 4.44 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
401 405 1.293062 AAGATGAGGGTGATGGCAGT 58.707 50.000 0.00 0.00 0.00 4.40
477 482 3.953612 AGTCTGGACAAGAGAGAGCATAG 59.046 47.826 3.51 0.00 34.84 2.23
483 488 4.202111 GGACAAGAGAGAGCATAGGAAGTC 60.202 50.000 0.00 0.00 0.00 3.01
501 506 2.366916 AGTCGGGCTGATTGATAAGAGG 59.633 50.000 0.00 0.00 0.00 3.69
507 512 3.501445 GGCTGATTGATAAGAGGCATGAC 59.499 47.826 0.00 0.00 0.00 3.06
508 513 3.186001 GCTGATTGATAAGAGGCATGACG 59.814 47.826 0.00 0.00 0.00 4.35
513 518 2.625314 TGATAAGAGGCATGACGGAGAG 59.375 50.000 0.00 0.00 0.00 3.20
633 641 0.695924 TGGGTACTGATGGGTTGGTG 59.304 55.000 0.00 0.00 0.00 4.17
634 642 0.034477 GGGTACTGATGGGTTGGTGG 60.034 60.000 0.00 0.00 0.00 4.61
635 643 0.034477 GGTACTGATGGGTTGGTGGG 60.034 60.000 0.00 0.00 0.00 4.61
655 663 4.080807 TGGGAGTTTAGTTGAAGTGTCACA 60.081 41.667 5.62 0.00 31.90 3.58
658 666 4.451900 AGTTTAGTTGAAGTGTCACAGGG 58.548 43.478 5.62 0.00 31.90 4.45
720 729 2.091333 GGGAGAAATGGCCCCAAATCTA 60.091 50.000 0.00 0.00 39.89 1.98
723 732 4.473444 GAGAAATGGCCCCAAATCTATGA 58.527 43.478 0.00 0.00 0.00 2.15
734 743 5.002516 CCCAAATCTATGAGCTCTGGATTC 58.997 45.833 16.19 0.00 0.00 2.52
753 762 6.168389 GGATTCTGGTTGCTTGATTTTGATT 58.832 36.000 0.00 0.00 0.00 2.57
762 771 7.096065 GGTTGCTTGATTTTGATTTGACAGTAC 60.096 37.037 0.00 0.00 0.00 2.73
810 821 8.682128 TTGAATTATTGTGTAAAATTCTCGCC 57.318 30.769 8.10 0.00 0.00 5.54
817 828 6.249035 TGTGTAAAATTCTCGCCTTAAAGG 57.751 37.500 0.00 0.00 38.80 3.11
835 846 7.116805 CCTTAAAGGTTTGAGCAATGTGAAATC 59.883 37.037 0.00 0.00 0.00 2.17
836 847 4.164822 AGGTTTGAGCAATGTGAAATCG 57.835 40.909 0.00 0.00 0.00 3.34
848 859 5.947228 ATGTGAAATCGTGTGATTGAAGT 57.053 34.783 0.00 0.00 44.02 3.01
892 903 8.125448 CAGTAACAATGGCTAGATTTAAGCTTC 58.875 37.037 0.00 0.00 39.97 3.86
984 995 5.105567 TGACCTTTGGTGACTGTTAGAAA 57.894 39.130 0.00 0.00 35.25 2.52
991 1002 3.139077 GGTGACTGTTAGAAACCACAGG 58.861 50.000 4.44 0.00 44.12 4.00
993 1004 1.798813 GACTGTTAGAAACCACAGGCG 59.201 52.381 4.44 0.00 44.12 5.52
1086 1097 3.280295 TGAGAGGTACGAAGAGATGGTC 58.720 50.000 0.00 0.00 0.00 4.02
1155 1166 2.097038 CGAGGAGCGCAACCTTCTG 61.097 63.158 23.11 14.29 37.93 3.02
1359 1370 1.208165 ACCTTGTCCCCTCATCCACC 61.208 60.000 0.00 0.00 0.00 4.61
1407 1418 6.617371 ACCTGAAGATGAAGGGTGATTACTAT 59.383 38.462 0.00 0.00 37.94 2.12
1446 1457 0.950116 GGCATAGAGTTCCTGCATGC 59.050 55.000 11.82 11.82 40.96 4.06
1449 1460 2.290093 GCATAGAGTTCCTGCATGCTTC 59.710 50.000 20.33 6.97 39.09 3.86
1465 1476 6.183360 TGCATGCTTCCTTCATTGCATATTAA 60.183 34.615 20.33 0.00 43.24 1.40
1471 1491 8.758715 GCTTCCTTCATTGCATATTAAATTGAC 58.241 33.333 0.00 0.00 0.00 3.18
1474 1494 8.632679 TCCTTCATTGCATATTAAATTGACTCC 58.367 33.333 0.00 0.00 0.00 3.85
1489 1509 6.764308 ATTGACTCCTTGGTTGAATGTATG 57.236 37.500 0.00 0.00 0.00 2.39
1490 1510 5.241403 TGACTCCTTGGTTGAATGTATGT 57.759 39.130 0.00 0.00 0.00 2.29
1492 1512 6.068010 TGACTCCTTGGTTGAATGTATGTTT 58.932 36.000 0.00 0.00 0.00 2.83
1494 1514 6.981722 ACTCCTTGGTTGAATGTATGTTTTC 58.018 36.000 0.00 0.00 0.00 2.29
1495 1515 6.777580 ACTCCTTGGTTGAATGTATGTTTTCT 59.222 34.615 0.00 0.00 0.00 2.52
1509 1530 7.853299 TGTATGTTTTCTATAGGTACCTTGCA 58.147 34.615 22.11 1.66 0.00 4.08
1583 1604 0.036732 TACAAAGCTGCTCAGGTGGG 59.963 55.000 1.00 1.23 39.39 4.61
1593 1614 3.673484 CAGGTGGGTTGCTTGCCG 61.673 66.667 0.00 0.00 0.00 5.69
1705 1742 7.441836 TCTCTTGCTCAGTTGAGTTTATGTTA 58.558 34.615 10.57 0.00 43.85 2.41
1708 1745 8.342634 TCTTGCTCAGTTGAGTTTATGTTAAAC 58.657 33.333 10.57 2.63 43.85 2.01
1849 1886 1.470632 CGCCAAGCAGGTTTGTTTTCA 60.471 47.619 0.00 0.00 40.61 2.69
1869 1906 4.905429 TCAACAATAACCTGCTGAGCTTA 58.095 39.130 5.83 0.00 0.00 3.09
1960 2013 8.959548 TGATATTTGTGCTTGATAATTGTGACT 58.040 29.630 0.00 0.00 0.00 3.41
2009 2097 4.094442 GCTAACAAGGTACCAGTGTTATGC 59.906 45.833 28.01 26.59 37.17 3.14
2055 2143 5.520376 AAAGGATGTTGTTGAACCTGAAG 57.480 39.130 0.00 0.00 0.00 3.02
2059 2147 3.644966 TGTTGTTGAACCTGAAGGACT 57.355 42.857 2.62 0.00 38.94 3.85
2266 2421 1.734477 CCTGACGCTGTGGACTTCG 60.734 63.158 0.00 0.00 0.00 3.79
2287 2442 3.181490 CGGACATCTCGGTACTTCATTCA 60.181 47.826 0.00 0.00 0.00 2.57
2292 2447 3.371034 TCTCGGTACTTCATTCATCCCA 58.629 45.455 0.00 0.00 0.00 4.37
2301 2456 4.079558 ACTTCATTCATCCCAAGCATACCT 60.080 41.667 0.00 0.00 0.00 3.08
2310 2465 1.614051 CCAAGCATACCTTCACCTGCA 60.614 52.381 0.00 0.00 37.09 4.41
2323 2478 3.921104 TCACCTGCATCCTATCTTCTCT 58.079 45.455 0.00 0.00 0.00 3.10
2324 2479 5.066913 TCACCTGCATCCTATCTTCTCTA 57.933 43.478 0.00 0.00 0.00 2.43
2327 2483 5.183713 CACCTGCATCCTATCTTCTCTAGAG 59.816 48.000 13.98 13.98 36.02 2.43
2333 2489 7.508636 TGCATCCTATCTTCTCTAGAGTCAATT 59.491 37.037 19.21 5.18 36.02 2.32
2489 2645 6.944557 TGTTCAGTGTAGATTGTAATGTCG 57.055 37.500 0.00 0.00 0.00 4.35
2499 2655 2.512485 TGTAATGTCGTCGTGGTTGT 57.488 45.000 0.00 0.00 0.00 3.32
2562 2718 4.112341 GCTGCCTTGCTTGCTCGG 62.112 66.667 0.00 0.00 0.00 4.63
2620 2776 7.222000 TCTTGTTGAACCTTTGTGTTACTTT 57.778 32.000 0.00 0.00 0.00 2.66
2663 2819 0.467290 TGCTCTTGTTTGTGACCCCC 60.467 55.000 0.00 0.00 0.00 5.40
2666 2822 0.467290 TCTTGTTTGTGACCCCCTGC 60.467 55.000 0.00 0.00 0.00 4.85
2670 2826 0.759060 GTTTGTGACCCCCTGCCTTT 60.759 55.000 0.00 0.00 0.00 3.11
3162 3326 3.428452 CCATTAACCGCTCGAGTCTTGTA 60.428 47.826 15.13 0.00 0.00 2.41
3163 3327 2.907910 TAACCGCTCGAGTCTTGTAC 57.092 50.000 15.13 0.00 0.00 2.90
3164 3328 0.243095 AACCGCTCGAGTCTTGTACC 59.757 55.000 15.13 0.00 0.00 3.34
3165 3329 1.139095 CCGCTCGAGTCTTGTACCC 59.861 63.158 15.13 0.00 0.00 3.69
3166 3330 1.226323 CGCTCGAGTCTTGTACCCG 60.226 63.158 15.13 1.42 0.00 5.28
3167 3331 1.516603 GCTCGAGTCTTGTACCCGC 60.517 63.158 15.13 0.00 0.00 6.13
3168 3332 1.139095 CTCGAGTCTTGTACCCGCC 59.861 63.158 3.62 0.00 0.00 6.13
3169 3333 2.202570 CGAGTCTTGTACCCGCCG 60.203 66.667 0.00 0.00 0.00 6.46
3170 3334 2.968206 GAGTCTTGTACCCGCCGT 59.032 61.111 0.00 0.00 0.00 5.68
3171 3335 1.291272 GAGTCTTGTACCCGCCGTT 59.709 57.895 0.00 0.00 0.00 4.44
3172 3336 1.005394 AGTCTTGTACCCGCCGTTG 60.005 57.895 0.00 0.00 0.00 4.10
3173 3337 2.030958 GTCTTGTACCCGCCGTTGG 61.031 63.158 0.00 0.00 0.00 3.77
3174 3338 3.428282 CTTGTACCCGCCGTTGGC 61.428 66.667 0.00 0.00 46.75 4.52
3184 3348 4.492604 CCGTTGGCAGGAAGGAAA 57.507 55.556 0.00 0.00 0.00 3.13
3185 3349 2.257353 CCGTTGGCAGGAAGGAAAG 58.743 57.895 0.00 0.00 0.00 2.62
3186 3350 0.250727 CCGTTGGCAGGAAGGAAAGA 60.251 55.000 0.00 0.00 0.00 2.52
3187 3351 1.604604 CGTTGGCAGGAAGGAAAGAA 58.395 50.000 0.00 0.00 0.00 2.52
3188 3352 1.537202 CGTTGGCAGGAAGGAAAGAAG 59.463 52.381 0.00 0.00 0.00 2.85
3189 3353 1.270826 GTTGGCAGGAAGGAAAGAAGC 59.729 52.381 0.00 0.00 0.00 3.86
3190 3354 0.773644 TGGCAGGAAGGAAAGAAGCT 59.226 50.000 0.00 0.00 0.00 3.74
3191 3355 1.271597 TGGCAGGAAGGAAAGAAGCTC 60.272 52.381 0.00 0.00 0.00 4.09
3192 3356 1.082690 GCAGGAAGGAAAGAAGCTCG 58.917 55.000 0.00 0.00 0.00 5.03
3193 3357 1.338200 GCAGGAAGGAAAGAAGCTCGA 60.338 52.381 0.00 0.00 0.00 4.04
3194 3358 2.615869 CAGGAAGGAAAGAAGCTCGAG 58.384 52.381 8.45 8.45 0.00 4.04
3195 3359 2.028567 CAGGAAGGAAAGAAGCTCGAGT 60.029 50.000 15.13 0.00 0.00 4.18
3196 3360 2.232696 AGGAAGGAAAGAAGCTCGAGTC 59.767 50.000 15.13 4.49 0.00 3.36
3197 3361 2.232696 GGAAGGAAAGAAGCTCGAGTCT 59.767 50.000 15.13 7.03 0.00 3.24
3198 3362 3.306433 GGAAGGAAAGAAGCTCGAGTCTT 60.306 47.826 15.13 16.88 35.59 3.01
3199 3363 3.311486 AGGAAAGAAGCTCGAGTCTTG 57.689 47.619 21.51 0.00 34.33 3.02
3200 3364 2.630580 AGGAAAGAAGCTCGAGTCTTGT 59.369 45.455 21.51 16.53 34.33 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 199 2.434185 GATGGAGACGGCGTGCAA 60.434 61.111 21.19 2.45 0.00 4.08
260 261 2.121506 TGCCTTCCCCTTCCCTGT 60.122 61.111 0.00 0.00 0.00 4.00
401 405 1.279025 GCCCACCTCCACCCTTATCA 61.279 60.000 0.00 0.00 0.00 2.15
436 440 1.740025 CTAGCTGTTAGGCAAACCAGC 59.260 52.381 0.00 8.98 40.01 4.85
477 482 2.910688 TATCAATCAGCCCGACTTCC 57.089 50.000 0.00 0.00 0.00 3.46
483 488 1.202687 TGCCTCTTATCAATCAGCCCG 60.203 52.381 0.00 0.00 0.00 6.13
501 506 1.142748 CACTCCCTCTCCGTCATGC 59.857 63.158 0.00 0.00 0.00 4.06
507 512 2.055042 CAGTCCCACTCCCTCTCCG 61.055 68.421 0.00 0.00 0.00 4.63
508 513 2.363172 GCAGTCCCACTCCCTCTCC 61.363 68.421 0.00 0.00 0.00 3.71
513 518 2.352805 CCTTGCAGTCCCACTCCC 59.647 66.667 0.00 0.00 0.00 4.30
633 641 4.448210 TGTGACACTTCAACTAAACTCCC 58.552 43.478 7.20 0.00 31.90 4.30
634 642 4.511826 CCTGTGACACTTCAACTAAACTCC 59.488 45.833 7.20 0.00 31.90 3.85
635 643 4.511826 CCCTGTGACACTTCAACTAAACTC 59.488 45.833 7.20 0.00 31.90 3.01
677 685 3.700539 CCAAAGTGATTCCATGTGCCATA 59.299 43.478 0.00 0.00 0.00 2.74
693 702 0.252239 GGGCCATTTCTCCCCAAAGT 60.252 55.000 4.39 0.00 38.70 2.66
720 729 2.683152 GCAACCAGAATCCAGAGCTCAT 60.683 50.000 17.77 0.00 0.00 2.90
723 732 0.990374 AGCAACCAGAATCCAGAGCT 59.010 50.000 0.00 0.00 0.00 4.09
734 743 5.754406 TGTCAAATCAAAATCAAGCAACCAG 59.246 36.000 0.00 0.00 0.00 4.00
753 762 6.935741 AAGCAACAAACTATGTACTGTCAA 57.064 33.333 0.00 0.00 42.99 3.18
762 771 7.704472 TCAAACCAACTTAAGCAACAAACTATG 59.296 33.333 1.29 0.00 0.00 2.23
768 777 9.606631 AATAATTCAAACCAACTTAAGCAACAA 57.393 25.926 1.29 0.00 0.00 2.83
810 821 7.148918 CGATTTCACATTGCTCAAACCTTTAAG 60.149 37.037 0.00 0.00 0.00 1.85
817 828 4.146961 CACACGATTTCACATTGCTCAAAC 59.853 41.667 0.00 0.00 0.00 2.93
835 846 2.545526 AGCTTGACACTTCAATCACACG 59.454 45.455 0.00 0.00 41.05 4.49
836 847 5.673337 TTAGCTTGACACTTCAATCACAC 57.327 39.130 0.00 0.00 41.05 3.82
848 859 8.896320 TGTTACTGAAGTAAATTAGCTTGACA 57.104 30.769 4.52 0.00 41.58 3.58
858 869 9.686683 AATCTAGCCATTGTTACTGAAGTAAAT 57.313 29.630 4.52 0.00 41.58 1.40
892 903 8.871862 CATTTCATTATTACAACAACCACATGG 58.128 33.333 0.00 0.00 42.17 3.66
984 995 1.003355 CATCTTCACCGCCTGTGGT 60.003 57.895 0.00 0.00 45.48 4.16
991 1002 3.869272 CTGCGCCATCTTCACCGC 61.869 66.667 4.18 0.00 45.99 5.68
1015 1026 1.056660 TTCTCCTCACGGGAAAGCTT 58.943 50.000 0.00 0.00 44.58 3.74
1086 1097 2.009042 GCCACCTTCTCCATGAACTCG 61.009 57.143 0.00 0.00 0.00 4.18
1155 1166 7.538678 CCAATAACATTCTTGTAAGCAACTGAC 59.461 37.037 0.00 0.00 34.06 3.51
1359 1370 1.216710 GACCTTGGACTCTGGAGCG 59.783 63.158 0.00 0.00 0.00 5.03
1407 1418 6.422344 TGCCGGTCATTATTGTAATACCTA 57.578 37.500 1.90 0.00 0.00 3.08
1424 1435 1.264749 TGCAGGAACTCTATGCCGGT 61.265 55.000 1.90 0.00 39.22 5.28
1427 1438 0.950116 GCATGCAGGAACTCTATGCC 59.050 55.000 14.21 0.00 44.23 4.40
1449 1460 8.636213 AGGAGTCAATTTAATATGCAATGAAGG 58.364 33.333 0.00 0.00 0.00 3.46
1465 1476 6.721208 ACATACATTCAACCAAGGAGTCAATT 59.279 34.615 0.00 0.00 0.00 2.32
1471 1491 7.219484 AGAAAACATACATTCAACCAAGGAG 57.781 36.000 0.00 0.00 0.00 3.69
1472 1492 8.877864 ATAGAAAACATACATTCAACCAAGGA 57.122 30.769 0.00 0.00 0.00 3.36
1485 1505 8.202137 TCTGCAAGGTACCTATAGAAAACATAC 58.798 37.037 16.67 0.00 0.00 2.39
1489 1509 6.641474 ACTCTGCAAGGTACCTATAGAAAAC 58.359 40.000 16.67 0.00 0.00 2.43
1490 1510 6.869206 ACTCTGCAAGGTACCTATAGAAAA 57.131 37.500 16.67 0.00 0.00 2.29
1492 1512 5.955959 TGAACTCTGCAAGGTACCTATAGAA 59.044 40.000 16.67 1.93 0.00 2.10
1494 1514 5.854010 TGAACTCTGCAAGGTACCTATAG 57.146 43.478 16.67 13.61 0.00 1.31
1495 1515 5.955959 TCTTGAACTCTGCAAGGTACCTATA 59.044 40.000 16.67 3.61 42.24 1.31
1583 1604 0.313672 TGAAATCCACGGCAAGCAAC 59.686 50.000 0.00 0.00 0.00 4.17
1593 1614 5.652014 TCAATGTTAGGACCATGAAATCCAC 59.348 40.000 11.72 4.56 37.47 4.02
1859 1896 4.038522 GTCCAGATGTAGATAAGCTCAGCA 59.961 45.833 0.00 0.00 0.00 4.41
1869 1906 6.015856 CGGTTCTATTCAGTCCAGATGTAGAT 60.016 42.308 0.00 0.00 0.00 1.98
2009 2097 6.861065 ATTTGCCTATCCAACTGTATAACG 57.139 37.500 0.00 0.00 0.00 3.18
2173 2328 5.443230 TCAGAGAGTCCAGTTCTGAGATA 57.557 43.478 5.87 0.00 41.62 1.98
2179 2334 1.173043 CGCTCAGAGAGTCCAGTTCT 58.827 55.000 0.00 0.00 31.39 3.01
2266 2421 4.386867 TGAATGAAGTACCGAGATGTCC 57.613 45.455 0.00 0.00 0.00 4.02
2287 2442 2.092212 CAGGTGAAGGTATGCTTGGGAT 60.092 50.000 0.00 0.00 0.00 3.85
2292 2447 2.648059 GATGCAGGTGAAGGTATGCTT 58.352 47.619 0.00 0.00 39.42 3.91
2301 2456 4.293494 AGAGAAGATAGGATGCAGGTGAA 58.707 43.478 0.00 0.00 0.00 3.18
2344 2500 3.860754 GCAGCCAAGTAAAGCGGAATTTT 60.861 43.478 0.00 0.00 0.00 1.82
2357 2513 2.753029 GTCCTCCTGCAGCCAAGT 59.247 61.111 8.66 0.00 0.00 3.16
2489 2645 2.879646 TCCAATTACCAACAACCACGAC 59.120 45.455 0.00 0.00 0.00 4.34
2562 2718 3.050275 GCCCGATAATCAGGCCGC 61.050 66.667 0.00 0.00 41.00 6.53
2620 2776 6.760770 CAGCAGAAAATTTCTAAAACCACCAA 59.239 34.615 8.03 0.00 38.11 3.67
2663 2819 5.525378 GGTCATCTAGTGAATACAAAGGCAG 59.475 44.000 0.00 0.00 38.90 4.85
2666 2822 6.644347 ACTGGTCATCTAGTGAATACAAAGG 58.356 40.000 0.00 0.00 38.90 3.11
2670 2826 5.419542 GCAACTGGTCATCTAGTGAATACA 58.580 41.667 0.00 0.00 38.90 2.29
2960 3116 1.330234 TGCTTTGAATGCTTGGCTCA 58.670 45.000 4.67 0.00 0.00 4.26
3142 3303 3.428589 GGTACAAGACTCGAGCGGTTAAT 60.429 47.826 13.61 0.00 0.00 1.40
3167 3331 0.250727 TCTTTCCTTCCTGCCAACGG 60.251 55.000 0.00 0.00 0.00 4.44
3168 3332 1.537202 CTTCTTTCCTTCCTGCCAACG 59.463 52.381 0.00 0.00 0.00 4.10
3169 3333 1.270826 GCTTCTTTCCTTCCTGCCAAC 59.729 52.381 0.00 0.00 0.00 3.77
3170 3334 1.145738 AGCTTCTTTCCTTCCTGCCAA 59.854 47.619 0.00 0.00 0.00 4.52
3171 3335 0.773644 AGCTTCTTTCCTTCCTGCCA 59.226 50.000 0.00 0.00 0.00 4.92
3172 3336 1.458398 GAGCTTCTTTCCTTCCTGCC 58.542 55.000 0.00 0.00 0.00 4.85
3173 3337 1.082690 CGAGCTTCTTTCCTTCCTGC 58.917 55.000 0.00 0.00 0.00 4.85
3174 3338 2.028567 ACTCGAGCTTCTTTCCTTCCTG 60.029 50.000 13.61 0.00 0.00 3.86
3175 3339 2.232696 GACTCGAGCTTCTTTCCTTCCT 59.767 50.000 13.61 0.00 0.00 3.36
3176 3340 2.232696 AGACTCGAGCTTCTTTCCTTCC 59.767 50.000 13.61 0.00 0.00 3.46
3177 3341 3.586100 AGACTCGAGCTTCTTTCCTTC 57.414 47.619 13.61 0.00 0.00 3.46
3178 3342 3.070302 ACAAGACTCGAGCTTCTTTCCTT 59.930 43.478 13.61 0.76 29.23 3.36
3179 3343 2.630580 ACAAGACTCGAGCTTCTTTCCT 59.369 45.455 13.61 0.00 29.23 3.36
3180 3344 3.033368 ACAAGACTCGAGCTTCTTTCC 57.967 47.619 13.61 0.00 29.23 3.13
3181 3345 3.921630 GGTACAAGACTCGAGCTTCTTTC 59.078 47.826 13.61 0.81 29.23 2.62
3182 3346 3.306156 GGGTACAAGACTCGAGCTTCTTT 60.306 47.826 13.61 8.54 29.23 2.52
3183 3347 2.231721 GGGTACAAGACTCGAGCTTCTT 59.768 50.000 13.61 12.32 32.02 2.52
3184 3348 1.819903 GGGTACAAGACTCGAGCTTCT 59.180 52.381 13.61 5.99 0.00 2.85
3185 3349 2.281140 GGGTACAAGACTCGAGCTTC 57.719 55.000 13.61 3.30 0.00 3.86
3192 3356 1.012486 CAACGGCGGGTACAAGACTC 61.012 60.000 13.24 0.00 0.00 3.36
3193 3357 1.005394 CAACGGCGGGTACAAGACT 60.005 57.895 13.24 0.00 0.00 3.24
3194 3358 2.030958 CCAACGGCGGGTACAAGAC 61.031 63.158 13.24 0.00 0.00 3.01
3195 3359 2.344500 CCAACGGCGGGTACAAGA 59.656 61.111 13.24 0.00 0.00 3.02
3196 3360 3.428282 GCCAACGGCGGGTACAAG 61.428 66.667 13.24 0.00 39.62 3.16


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

AutoCloner maintained by Alex Coulton.