Multiple sequence alignment - TraesCS2D01G360200

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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 TraesCS2D01G360200 chr2D 100.000 4003 0 0 1 4003 462205177 462201175 0.000000e+00 7393.0
1 TraesCS2D01G360200 chr2A 91.494 2316 144 32 420 2714 607484294 607482011 0.000000e+00 3136.0
2 TraesCS2D01G360200 chr2A 91.773 1337 67 20 420 1749 610117777 610116477 0.000000e+00 1820.0
3 TraesCS2D01G360200 chr2A 89.959 1225 83 16 2808 4000 607482023 607480807 0.000000e+00 1544.0
4 TraesCS2D01G360200 chr2A 89.053 1215 103 14 2808 4001 610115493 610114288 0.000000e+00 1480.0
5 TraesCS2D01G360200 chr2A 89.939 656 47 10 1803 2454 610116358 610115718 0.000000e+00 828.0
6 TraesCS2D01G360200 chr2A 93.269 416 21 4 1 412 610118266 610117854 1.230000e-169 606.0
7 TraesCS2D01G360200 chr2A 92.086 417 19 6 1 412 607484778 607484371 3.470000e-160 575.0
8 TraesCS2D01G360200 chr2A 83.721 387 41 13 3204 3574 610114513 610114133 2.960000e-91 346.0
9 TraesCS2D01G360200 chr2A 89.431 123 9 2 2593 2714 610115600 610115481 6.930000e-33 152.0
10 TraesCS2D01G360200 chr2A 80.120 166 18 8 3657 3809 610115276 610115113 4.230000e-20 110.0
11 TraesCS2D01G360200 chr2A 78.182 165 19 6 3654 3802 607481808 607481645 5.510000e-14 89.8
12 TraesCS2D01G360200 chr2B 93.372 1388 58 15 1347 2714 544987547 544986174 0.000000e+00 2023.0
13 TraesCS2D01G360200 chr2B 91.360 544 24 13 416 958 544990775 544990254 0.000000e+00 723.0
14 TraesCS2D01G360200 chr2B 95.567 406 16 2 1 405 544991265 544990861 0.000000e+00 649.0
15 TraesCS2D01G360200 chr2B 96.053 380 13 2 2808 3186 544986186 544985808 5.680000e-173 617.0
16 TraesCS2D01G360200 chr2B 92.191 397 21 4 3204 3597 544985830 544985441 1.630000e-153 553.0
17 TraesCS2D01G360200 chr2B 94.183 361 14 4 969 1326 544987896 544987540 9.780000e-151 544.0
18 TraesCS2D01G360200 chr2B 83.598 378 37 17 3204 3564 544985322 544984953 8.290000e-87 331.0
19 TraesCS2D01G360200 chr2B 90.152 264 12 4 3750 4000 544985359 544985097 8.290000e-87 331.0
20 TraesCS2D01G360200 chr2B 78.443 334 40 14 3693 4003 544985933 544985609 5.280000e-44 189.0


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 TraesCS2D01G360200 chr2D 462201175 462205177 4002 True 7393.000000 7393 100.000000 1 4003 1 chr2D.!!$R1 4002
1 TraesCS2D01G360200 chr2A 607480807 607484778 3971 True 1336.200000 3136 87.930250 1 4000 4 chr2A.!!$R1 3999
2 TraesCS2D01G360200 chr2A 610114133 610118266 4133 True 763.142857 1820 88.186571 1 4001 7 chr2A.!!$R2 4000
3 TraesCS2D01G360200 chr2B 544984953 544991265 6312 True 662.222222 2023 90.546556 1 4003 9 chr2B.!!$R1 4002

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
406 422 0.031994 AACAAAACCTGGTCATGCGC 59.968 50.0 0.00 0.0 0.0 6.09 F
410 426 0.324943 AAACCTGGTCATGCGCTAGT 59.675 50.0 9.73 0.0 0.0 2.57 F
1521 3971 0.674895 ACTCTGCTGAAATGTCGGGC 60.675 55.0 0.00 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 3970 0.250901 TTCTGAACCCTGAAGCCAGC 60.251 55.0 0.0 0.0 39.07 4.85 R
2025 4559 1.189752 ACAGATGCTCGTGATCCTGT 58.810 50.0 0.0 0.0 0.00 4.00 R
3493 6071 0.111446 TGAACTGCCGAAATGGGGAA 59.889 50.0 0.0 0.0 38.63 3.97 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
83 90 2.251409 CAGCCCTCAGGATGTACATG 57.749 55.000 14.43 0.05 44.95 3.21
84 91 1.487976 CAGCCCTCAGGATGTACATGT 59.512 52.381 14.43 2.69 44.95 3.21
85 92 2.700371 CAGCCCTCAGGATGTACATGTA 59.300 50.000 14.43 0.08 44.95 2.29
175 190 2.253610 TCAGTACGGAATTCACCAGGT 58.746 47.619 7.93 0.00 0.00 4.00
231 246 6.978659 ACAATATGAGCAATGCATTTCAAGAG 59.021 34.615 15.80 9.85 0.00 2.85
385 401 4.585879 ACGCCTTTAGTATGAACATTGGT 58.414 39.130 0.00 0.00 0.00 3.67
388 404 6.655848 ACGCCTTTAGTATGAACATTGGTAAA 59.344 34.615 0.00 0.00 0.00 2.01
405 421 2.507339 AAACAAAACCTGGTCATGCG 57.493 45.000 0.00 0.00 0.00 4.73
406 422 0.031994 AACAAAACCTGGTCATGCGC 59.968 50.000 0.00 0.00 0.00 6.09
407 423 0.823356 ACAAAACCTGGTCATGCGCT 60.823 50.000 9.73 0.00 0.00 5.92
408 424 1.164411 CAAAACCTGGTCATGCGCTA 58.836 50.000 9.73 0.00 0.00 4.26
409 425 1.131126 CAAAACCTGGTCATGCGCTAG 59.869 52.381 9.73 0.14 0.00 3.42
410 426 0.324943 AAACCTGGTCATGCGCTAGT 59.675 50.000 9.73 0.00 0.00 2.57
412 428 0.324943 ACCTGGTCATGCGCTAGTTT 59.675 50.000 9.73 0.00 0.00 2.66
413 429 1.271379 ACCTGGTCATGCGCTAGTTTT 60.271 47.619 9.73 0.00 0.00 2.43
415 431 3.006940 CCTGGTCATGCGCTAGTTTTTA 58.993 45.455 9.73 0.00 0.00 1.52
416 432 3.181510 CCTGGTCATGCGCTAGTTTTTAC 60.182 47.826 9.73 0.00 0.00 2.01
418 434 4.006989 TGGTCATGCGCTAGTTTTTACAT 58.993 39.130 9.73 0.00 0.00 2.29
444 538 7.659290 ACAGTTTTGTTTCGAAATTTACTCG 57.341 32.000 14.69 11.42 32.28 4.18
662 756 1.289380 GGAGAAGAGCGACACGGTT 59.711 57.895 0.00 0.00 37.83 4.44
687 781 4.719106 GGTCCTGCTGCTGCTGCT 62.719 66.667 27.67 0.00 40.48 4.24
816 910 1.521457 CACGACCCCACATCCATCG 60.521 63.158 0.00 0.00 38.71 3.84
818 912 2.911143 GACCCCACATCCATCGCT 59.089 61.111 0.00 0.00 0.00 4.93
845 940 2.444706 CTCTCCCCCGGATGCAGA 60.445 66.667 0.73 0.00 0.00 4.26
850 945 3.083349 CCCCGGATGCAGACCTCA 61.083 66.667 0.73 0.00 0.00 3.86
906 1001 1.135575 GCTCCCAAATCGTTGAGCTTG 60.136 52.381 0.00 0.00 36.83 4.01
909 1004 1.135575 CCCAAATCGTTGAGCTTGAGC 60.136 52.381 0.00 0.00 36.83 4.26
982 3425 1.228245 CCTAATCATGTGGCGGGGG 60.228 63.158 0.00 0.00 0.00 5.40
1223 3670 3.425404 GCATTGGCAAATACGTACTGTG 58.575 45.455 3.01 0.00 40.72 3.66
1273 3720 2.598632 GCAGCTCAACGACGTGCTT 61.599 57.895 8.44 0.00 33.63 3.91
1334 3781 4.080919 TCTCTTGGTCAATGTACATCCCTG 60.081 45.833 9.23 4.19 0.00 4.45
1346 3793 2.786495 ATCCCTGGTGCTAGTCGCG 61.786 63.158 0.00 0.00 43.27 5.87
1383 3833 2.863809 AGACAACTGGTTGATGGGAAC 58.136 47.619 18.63 0.00 42.93 3.62
1471 3921 1.468914 GATTTGGCGTTCCTTCTGTCC 59.531 52.381 0.00 0.00 0.00 4.02
1520 3970 2.271800 GTACTCTGCTGAAATGTCGGG 58.728 52.381 0.00 0.00 0.00 5.14
1521 3971 0.674895 ACTCTGCTGAAATGTCGGGC 60.675 55.000 0.00 0.00 0.00 6.13
1552 4010 5.009410 CAGGGTTCAGAATATCCAAGCAATC 59.991 44.000 0.00 0.00 0.00 2.67
1557 4015 8.037166 GGTTCAGAATATCCAAGCAATCTTTTT 58.963 33.333 0.00 0.00 0.00 1.94
1562 4021 2.969628 TCCAAGCAATCTTTTTGGGGA 58.030 42.857 2.96 0.00 41.31 4.81
1581 4040 3.152341 GGATGGCAATCTTATGGTCCAG 58.848 50.000 0.00 0.00 32.95 3.86
1602 4061 2.430465 CCTCTCAAATGTCACAGGTGG 58.570 52.381 0.00 0.00 0.00 4.61
1649 4108 3.499737 CAAACCGCTGCTAGCCGG 61.500 66.667 25.18 25.18 38.18 6.13
1788 4259 4.457257 GCTTGTCTTTTGATCAGGCTAACT 59.543 41.667 0.00 0.00 33.43 2.24
1865 4399 3.773418 TGATTTACCTTTCACGGACCA 57.227 42.857 0.00 0.00 0.00 4.02
1938 4472 2.901839 ACCCAAAGCAATGCAAGAGATT 59.098 40.909 8.35 0.00 0.00 2.40
1982 4516 2.033675 GGGTGTACGGTTCAAGTTTTGG 59.966 50.000 0.00 0.00 0.00 3.28
2025 4559 7.685481 TCTCATGATTTGGTTTTACTGGACTA 58.315 34.615 0.00 0.00 0.00 2.59
2194 4729 2.989909 TCCACCATGACATTGTAGCAG 58.010 47.619 0.00 0.00 0.00 4.24
2200 4735 5.298527 CACCATGACATTGTAGCAGAATCAT 59.701 40.000 0.00 0.00 0.00 2.45
2254 4789 6.670077 GGAACTGATCCTAACAATTCTCAC 57.330 41.667 0.00 0.00 45.56 3.51
2255 4790 6.410540 GGAACTGATCCTAACAATTCTCACT 58.589 40.000 0.00 0.00 45.56 3.41
2256 4791 7.556844 GGAACTGATCCTAACAATTCTCACTA 58.443 38.462 0.00 0.00 45.56 2.74
2257 4792 8.041323 GGAACTGATCCTAACAATTCTCACTAA 58.959 37.037 0.00 0.00 45.56 2.24
2258 4793 8.779354 AACTGATCCTAACAATTCTCACTAAC 57.221 34.615 0.00 0.00 0.00 2.34
2259 4794 8.140112 ACTGATCCTAACAATTCTCACTAACT 57.860 34.615 0.00 0.00 0.00 2.24
2446 4988 8.768019 ACAGAAAATATATCACGTCATCATGTG 58.232 33.333 0.00 0.00 40.49 3.21
2714 5279 2.308570 TGGAGTGGTATGTGCCATTTCT 59.691 45.455 0.00 0.00 41.08 2.52
2715 5280 3.245229 TGGAGTGGTATGTGCCATTTCTT 60.245 43.478 0.00 0.00 41.08 2.52
2716 5281 3.763897 GGAGTGGTATGTGCCATTTCTTT 59.236 43.478 0.00 0.00 41.08 2.52
2717 5282 4.220602 GGAGTGGTATGTGCCATTTCTTTT 59.779 41.667 0.00 0.00 41.08 2.27
2718 5283 5.279456 GGAGTGGTATGTGCCATTTCTTTTT 60.279 40.000 0.00 0.00 41.08 1.94
2736 5301 2.559698 TTTTCGAACCATGCAGGAGA 57.440 45.000 0.00 0.00 41.22 3.71
2737 5302 2.559698 TTTCGAACCATGCAGGAGAA 57.440 45.000 0.00 4.57 41.22 2.87
2738 5303 2.787473 TTCGAACCATGCAGGAGAAT 57.213 45.000 0.00 0.00 41.22 2.40
2739 5304 2.787473 TCGAACCATGCAGGAGAATT 57.213 45.000 0.00 0.00 41.22 2.17
2740 5305 2.358957 TCGAACCATGCAGGAGAATTG 58.641 47.619 0.00 0.00 41.22 2.32
2741 5306 1.202222 CGAACCATGCAGGAGAATTGC 60.202 52.381 0.00 0.00 41.22 3.56
2753 5318 8.640063 TGCAGGAGAATTGCATGTATTATATT 57.360 30.769 0.00 0.00 45.89 1.28
2754 5319 9.737844 TGCAGGAGAATTGCATGTATTATATTA 57.262 29.630 0.00 0.00 45.89 0.98
2783 5348 9.831054 GATAGAAAAGATGTAAAATACGTCACG 57.169 33.333 11.21 0.00 45.05 4.35
2784 5349 7.878477 AGAAAAGATGTAAAATACGTCACGA 57.122 32.000 2.91 0.00 45.05 4.35
2785 5350 7.727017 AGAAAAGATGTAAAATACGTCACGAC 58.273 34.615 2.91 0.00 45.05 4.34
2786 5351 6.399204 AAAGATGTAAAATACGTCACGACC 57.601 37.500 2.91 0.00 45.05 4.79
2787 5352 5.320549 AGATGTAAAATACGTCACGACCT 57.679 39.130 2.91 0.00 45.05 3.85
2788 5353 5.100259 AGATGTAAAATACGTCACGACCTG 58.900 41.667 2.91 0.00 45.05 4.00
2789 5354 4.241590 TGTAAAATACGTCACGACCTGT 57.758 40.909 2.91 0.00 0.00 4.00
2790 5355 4.229096 TGTAAAATACGTCACGACCTGTC 58.771 43.478 2.91 0.00 0.00 3.51
2791 5356 2.358939 AAATACGTCACGACCTGTCC 57.641 50.000 2.91 0.00 0.00 4.02
2792 5357 0.169672 AATACGTCACGACCTGTCCG 59.830 55.000 2.91 0.00 0.00 4.79
2793 5358 0.674581 ATACGTCACGACCTGTCCGA 60.675 55.000 2.91 0.00 0.00 4.55
2794 5359 0.674581 TACGTCACGACCTGTCCGAT 60.675 55.000 2.91 0.00 0.00 4.18
2795 5360 0.674581 ACGTCACGACCTGTCCGATA 60.675 55.000 2.91 0.00 0.00 2.92
2796 5361 0.448990 CGTCACGACCTGTCCGATAA 59.551 55.000 0.00 0.00 0.00 1.75
2797 5362 1.065102 CGTCACGACCTGTCCGATAAT 59.935 52.381 0.00 0.00 0.00 1.28
2798 5363 2.479049 CGTCACGACCTGTCCGATAATT 60.479 50.000 0.00 0.00 0.00 1.40
2799 5364 3.518590 GTCACGACCTGTCCGATAATTT 58.481 45.455 0.00 0.00 0.00 1.82
2800 5365 4.675510 GTCACGACCTGTCCGATAATTTA 58.324 43.478 0.00 0.00 0.00 1.40
2801 5366 4.738740 GTCACGACCTGTCCGATAATTTAG 59.261 45.833 0.00 0.00 0.00 1.85
2802 5367 4.400251 TCACGACCTGTCCGATAATTTAGT 59.600 41.667 0.00 0.00 0.00 2.24
2803 5368 5.589855 TCACGACCTGTCCGATAATTTAGTA 59.410 40.000 0.00 0.00 0.00 1.82
2804 5369 5.913514 CACGACCTGTCCGATAATTTAGTAG 59.086 44.000 0.00 0.00 0.00 2.57
2805 5370 5.824624 ACGACCTGTCCGATAATTTAGTAGA 59.175 40.000 0.00 0.00 0.00 2.59
2806 5371 6.141462 CGACCTGTCCGATAATTTAGTAGAC 58.859 44.000 0.00 0.00 0.00 2.59
2807 5372 6.017275 CGACCTGTCCGATAATTTAGTAGACT 60.017 42.308 0.00 0.00 0.00 3.24
2808 5373 7.172190 CGACCTGTCCGATAATTTAGTAGACTA 59.828 40.741 0.00 0.00 0.00 2.59
2809 5374 8.937207 ACCTGTCCGATAATTTAGTAGACTAT 57.063 34.615 0.00 0.00 0.00 2.12
2810 5375 8.794553 ACCTGTCCGATAATTTAGTAGACTATG 58.205 37.037 0.00 0.00 0.00 2.23
2811 5376 8.794553 CCTGTCCGATAATTTAGTAGACTATGT 58.205 37.037 0.00 0.00 0.00 2.29
2815 5380 9.797642 TCCGATAATTTAGTAGACTATGTACCA 57.202 33.333 0.00 0.00 0.00 3.25
2839 5404 7.987458 CCATTTCACCAATGACTATGTACTACT 59.013 37.037 0.00 0.00 44.78 2.57
2926 5491 2.303311 AGGAGTTGGAGAAGTTAGCCAC 59.697 50.000 0.00 0.00 0.00 5.01
2957 5522 2.185004 TTTCCTCAGCCAAGCACTAC 57.815 50.000 0.00 0.00 0.00 2.73
3130 5703 1.969923 CCAATGCTTCAAACCTCCCAA 59.030 47.619 0.00 0.00 0.00 4.12
3172 5746 7.651704 GCTTGAACAATAAAACAACACACCTAT 59.348 33.333 0.00 0.00 0.00 2.57
3229 5803 3.192422 CCTACGGCATGGAAATCAAAACA 59.808 43.478 0.00 0.00 0.00 2.83
3314 5888 3.054503 CAGGTGTGCTGCTCTGCC 61.055 66.667 0.00 4.64 0.00 4.85
3340 5914 6.944862 ACTTCTGAGCAATAAGACTGGAAATT 59.055 34.615 0.00 0.00 0.00 1.82
3362 5937 2.298729 GGGCATAAAAACAAGCACCTCA 59.701 45.455 0.00 0.00 0.00 3.86
3365 5940 4.321899 GGCATAAAAACAAGCACCTCATCA 60.322 41.667 0.00 0.00 0.00 3.07
3418 5996 4.156455 TGATAGGTGAGAATTTCAGGCC 57.844 45.455 0.00 0.00 36.21 5.19
3493 6071 1.906574 TGCCCTCCTCTGTTTATTCGT 59.093 47.619 0.00 0.00 0.00 3.85
3537 6115 9.823647 CAGATCTACACTGGAGTATTTATGTTT 57.176 33.333 0.00 0.00 0.00 2.83
3558 6138 8.597662 TGTTTAGTGATTTTACCAGTGACTAC 57.402 34.615 0.00 0.00 0.00 2.73
3572 6152 4.809426 CAGTGACTACGGTGAAACTTCTTT 59.191 41.667 0.00 0.00 36.74 2.52
3594 6174 3.006110 TGGTTAAACTCGATGAACGACCT 59.994 43.478 0.00 0.00 46.45 3.85
3627 6207 4.444536 TCGCAGTAAAACACAAGTAACCT 58.555 39.130 0.00 0.00 0.00 3.50
3648 6228 1.872313 CCTACTAGGAGTCTAACGCCG 59.128 57.143 0.11 0.00 43.27 6.46
3700 6283 9.898152 TTTTAAGTTTGTGAATCCATTTTCCTT 57.102 25.926 0.00 0.00 0.00 3.36
3747 6331 3.747388 GCTGATCCCATTCGGAACCAATA 60.747 47.826 0.00 0.00 46.47 1.90
3765 6358 0.698238 TACCCCAGCTGTGCATTTCT 59.302 50.000 13.81 0.00 0.00 2.52
3950 6556 0.898320 ACCTCCTCGTCTGATTGGTG 59.102 55.000 0.00 0.00 0.00 4.17
3969 6575 0.110486 GACTGGAACTGGGAAGGCAA 59.890 55.000 0.00 0.00 0.00 4.52
4001 6607 2.555227 GGTGAGAATTTCAGGCCCTGAA 60.555 50.000 22.25 22.25 46.93 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 5.703592 TGTATGACCAAATTACACAGGTGTC 59.296 40.000 8.56 0.00 43.74 3.67
207 222 6.420903 CCTCTTGAAATGCATTGCTCATATTG 59.579 38.462 18.39 7.85 0.00 1.90
231 246 0.324943 TTGGGTTGCTCTGCTAGTCC 59.675 55.000 0.00 0.00 0.00 3.85
385 401 2.287909 GCGCATGACCAGGTTTTGTTTA 60.288 45.455 0.30 0.00 0.00 2.01
388 404 0.823356 AGCGCATGACCAGGTTTTGT 60.823 50.000 11.47 0.00 0.00 2.83
408 424 9.843334 TCGAAACAAAACTGTTATGTAAAAACT 57.157 25.926 0.00 0.00 0.00 2.66
418 434 9.212687 CGAGTAAATTTCGAAACAAAACTGTTA 57.787 29.630 13.81 0.00 40.36 2.41
443 537 4.025647 GCTTGCTACTGCTTTTACTATCCG 60.026 45.833 0.00 0.00 40.48 4.18
444 538 4.876107 TGCTTGCTACTGCTTTTACTATCC 59.124 41.667 0.00 0.00 40.48 2.59
800 894 1.744320 TAGCGATGGATGTGGGGTCG 61.744 60.000 0.00 0.00 35.56 4.79
809 903 1.528292 GCGAGGGTCTAGCGATGGAT 61.528 60.000 0.00 0.00 0.00 3.41
816 910 2.197605 GGGAGAGCGAGGGTCTAGC 61.198 68.421 0.00 0.00 40.67 3.42
818 912 2.601868 GGGGAGAGCGAGGGTCTA 59.398 66.667 0.00 0.00 40.67 2.59
906 1001 3.752339 CTTTTGCCCCTGCCGCTC 61.752 66.667 0.00 0.00 36.33 5.03
909 1004 2.282462 ACTCTTTTGCCCCTGCCG 60.282 61.111 0.00 0.00 36.33 5.69
982 3425 4.072088 CGGTGTCCGTTTGCTCGC 62.072 66.667 0.00 0.00 42.73 5.03
1247 3694 1.597854 CGTTGAGCTGCAAGGGACA 60.598 57.895 1.02 0.00 38.40 4.02
1250 3697 2.671177 CGTCGTTGAGCTGCAAGGG 61.671 63.158 1.02 5.31 41.47 3.95
1346 3793 7.301054 CAGTTGTCTTCTGAATTCACATTACC 58.699 38.462 3.38 0.00 35.20 2.85
1520 3970 0.250901 TTCTGAACCCTGAAGCCAGC 60.251 55.000 0.00 0.00 39.07 4.85
1521 3971 2.503895 ATTCTGAACCCTGAAGCCAG 57.496 50.000 0.00 0.00 40.09 4.85
1552 4010 3.986996 AAGATTGCCATCCCCAAAAAG 57.013 42.857 0.00 0.00 0.00 2.27
1557 4015 1.858910 ACCATAAGATTGCCATCCCCA 59.141 47.619 0.00 0.00 0.00 4.96
1562 4021 2.590821 GCTGGACCATAAGATTGCCAT 58.409 47.619 0.00 0.00 0.00 4.40
1581 4040 1.808945 CACCTGTGACATTTGAGAGGC 59.191 52.381 0.00 0.00 0.00 4.70
1602 4061 1.676014 CCCTGAGAAATCGACACCCAC 60.676 57.143 0.00 0.00 0.00 4.61
1649 4108 2.281484 TTCCAGCGTTGGTCCTGC 60.281 61.111 18.51 0.00 45.26 4.85
1788 4259 3.009723 GTCTTAGCCAAGCACATAAGCA 58.990 45.455 0.00 0.00 36.85 3.91
1789 4260 3.009723 TGTCTTAGCCAAGCACATAAGC 58.990 45.455 0.00 0.00 0.00 3.09
1865 4399 5.106317 CCAACCGTAACAGCATCAAAGTAAT 60.106 40.000 0.00 0.00 0.00 1.89
1938 4472 5.012768 CCAACCTGGTTTTAGGACTCTAAGA 59.987 44.000 9.90 0.00 40.42 2.10
1982 4516 4.005650 TGAGAATTCATGCTGAACTGGAC 58.994 43.478 8.44 0.00 39.45 4.02
2017 4551 2.370349 CTCGTGATCCTGTAGTCCAGT 58.630 52.381 0.00 0.00 39.74 4.00
2025 4559 1.189752 ACAGATGCTCGTGATCCTGT 58.810 50.000 0.00 0.00 0.00 4.00
2446 4988 7.932120 AGTTCTTAGACACGCATTATGTATC 57.068 36.000 0.00 0.00 0.00 2.24
2448 4990 9.079833 GTTTAGTTCTTAGACACGCATTATGTA 57.920 33.333 0.00 0.00 0.00 2.29
2716 5281 2.857483 TCTCCTGCATGGTTCGAAAAA 58.143 42.857 0.00 0.00 37.07 1.94
2717 5282 2.559698 TCTCCTGCATGGTTCGAAAA 57.440 45.000 0.00 0.00 37.07 2.29
2718 5283 2.559698 TTCTCCTGCATGGTTCGAAA 57.440 45.000 0.00 0.00 37.07 3.46
2719 5284 2.749076 CAATTCTCCTGCATGGTTCGAA 59.251 45.455 0.00 0.00 37.07 3.71
2720 5285 2.358957 CAATTCTCCTGCATGGTTCGA 58.641 47.619 0.00 0.00 37.07 3.71
2721 5286 1.202222 GCAATTCTCCTGCATGGTTCG 60.202 52.381 0.00 0.00 39.69 3.95
2722 5287 1.820519 TGCAATTCTCCTGCATGGTTC 59.179 47.619 0.00 0.00 44.67 3.62
2723 5288 1.927487 TGCAATTCTCCTGCATGGTT 58.073 45.000 0.00 0.00 44.67 3.67
2724 5289 3.675995 TGCAATTCTCCTGCATGGT 57.324 47.368 0.00 0.00 44.67 3.55
2757 5322 9.831054 CGTGACGTATTTTACATCTTTTCTATC 57.169 33.333 0.00 0.00 0.00 2.08
2758 5323 9.577110 TCGTGACGTATTTTACATCTTTTCTAT 57.423 29.630 4.40 0.00 0.00 1.98
2759 5324 8.853345 GTCGTGACGTATTTTACATCTTTTCTA 58.147 33.333 4.40 0.00 0.00 2.10
2760 5325 7.148689 GGTCGTGACGTATTTTACATCTTTTCT 60.149 37.037 4.40 0.00 0.00 2.52
2761 5326 6.952083 GGTCGTGACGTATTTTACATCTTTTC 59.048 38.462 4.40 0.00 0.00 2.29
2762 5327 6.647895 AGGTCGTGACGTATTTTACATCTTTT 59.352 34.615 4.40 0.00 0.00 2.27
2763 5328 6.090358 CAGGTCGTGACGTATTTTACATCTTT 59.910 38.462 4.40 0.00 0.00 2.52
2764 5329 5.575606 CAGGTCGTGACGTATTTTACATCTT 59.424 40.000 4.40 0.00 0.00 2.40
2765 5330 5.100259 CAGGTCGTGACGTATTTTACATCT 58.900 41.667 4.40 0.00 0.00 2.90
2766 5331 4.860907 ACAGGTCGTGACGTATTTTACATC 59.139 41.667 4.40 0.00 0.00 3.06
2767 5332 4.813027 ACAGGTCGTGACGTATTTTACAT 58.187 39.130 4.40 0.00 0.00 2.29
2768 5333 4.229096 GACAGGTCGTGACGTATTTTACA 58.771 43.478 4.40 0.00 0.00 2.41
2769 5334 3.609807 GGACAGGTCGTGACGTATTTTAC 59.390 47.826 4.40 0.00 0.00 2.01
2770 5335 3.670359 CGGACAGGTCGTGACGTATTTTA 60.670 47.826 4.40 0.00 0.00 1.52
2771 5336 2.680577 GGACAGGTCGTGACGTATTTT 58.319 47.619 4.40 0.00 0.00 1.82
2772 5337 1.401931 CGGACAGGTCGTGACGTATTT 60.402 52.381 4.40 0.00 0.00 1.40
2773 5338 0.169672 CGGACAGGTCGTGACGTATT 59.830 55.000 4.40 0.00 0.00 1.89
2774 5339 0.674581 TCGGACAGGTCGTGACGTAT 60.675 55.000 4.40 0.00 33.69 3.06
2775 5340 0.674581 ATCGGACAGGTCGTGACGTA 60.675 55.000 4.40 0.00 33.69 3.57
2776 5341 0.674581 TATCGGACAGGTCGTGACGT 60.675 55.000 4.40 0.00 33.69 4.34
2777 5342 0.448990 TTATCGGACAGGTCGTGACG 59.551 55.000 0.00 0.00 0.00 4.35
2778 5343 2.865343 ATTATCGGACAGGTCGTGAC 57.135 50.000 0.00 0.00 0.00 3.67
2779 5344 3.880047 AAATTATCGGACAGGTCGTGA 57.120 42.857 0.00 0.00 0.00 4.35
2780 5345 4.679662 ACTAAATTATCGGACAGGTCGTG 58.320 43.478 0.00 0.00 0.00 4.35
2781 5346 4.996788 ACTAAATTATCGGACAGGTCGT 57.003 40.909 0.00 0.00 0.00 4.34
2782 5347 6.017275 AGTCTACTAAATTATCGGACAGGTCG 60.017 42.308 0.00 0.00 0.00 4.79
2783 5348 7.274603 AGTCTACTAAATTATCGGACAGGTC 57.725 40.000 0.00 0.00 0.00 3.85
2784 5349 8.794553 CATAGTCTACTAAATTATCGGACAGGT 58.205 37.037 0.00 0.00 31.39 4.00
2785 5350 8.794553 ACATAGTCTACTAAATTATCGGACAGG 58.205 37.037 0.00 0.00 31.39 4.00
2789 5354 9.797642 TGGTACATAGTCTACTAAATTATCGGA 57.202 33.333 0.00 0.00 31.39 4.55
2802 5367 7.985184 GTCATTGGTGAAATGGTACATAGTCTA 59.015 37.037 0.00 0.00 45.00 2.59
2803 5368 6.823689 GTCATTGGTGAAATGGTACATAGTCT 59.176 38.462 0.00 0.00 45.00 3.24
2804 5369 6.823689 AGTCATTGGTGAAATGGTACATAGTC 59.176 38.462 0.00 0.00 45.00 2.59
2805 5370 6.721318 AGTCATTGGTGAAATGGTACATAGT 58.279 36.000 0.00 0.00 45.00 2.12
2806 5371 8.777413 CATAGTCATTGGTGAAATGGTACATAG 58.223 37.037 0.00 0.00 45.00 2.23
2807 5372 8.271458 ACATAGTCATTGGTGAAATGGTACATA 58.729 33.333 0.00 0.00 45.00 2.29
2808 5373 7.118723 ACATAGTCATTGGTGAAATGGTACAT 58.881 34.615 0.00 0.00 45.00 2.29
2809 5374 6.480763 ACATAGTCATTGGTGAAATGGTACA 58.519 36.000 0.00 0.00 45.00 2.90
2810 5375 7.769044 AGTACATAGTCATTGGTGAAATGGTAC 59.231 37.037 0.00 0.00 45.00 3.34
2811 5376 7.857456 AGTACATAGTCATTGGTGAAATGGTA 58.143 34.615 0.00 0.00 45.00 3.25
2812 5377 6.721318 AGTACATAGTCATTGGTGAAATGGT 58.279 36.000 0.00 0.00 45.00 3.55
2813 5378 7.987458 AGTAGTACATAGTCATTGGTGAAATGG 59.013 37.037 2.52 0.00 45.00 3.16
2814 5379 8.948631 AGTAGTACATAGTCATTGGTGAAATG 57.051 34.615 2.52 0.00 46.10 2.32
2815 5380 9.959721 AAAGTAGTACATAGTCATTGGTGAAAT 57.040 29.630 2.52 0.00 35.80 2.17
2816 5381 9.431887 GAAAGTAGTACATAGTCATTGGTGAAA 57.568 33.333 2.52 0.00 35.80 2.69
2817 5382 8.590204 TGAAAGTAGTACATAGTCATTGGTGAA 58.410 33.333 2.52 0.00 35.80 3.18
2818 5383 8.033038 GTGAAAGTAGTACATAGTCATTGGTGA 58.967 37.037 2.52 0.00 0.00 4.02
2819 5384 7.009265 CGTGAAAGTAGTACATAGTCATTGGTG 59.991 40.741 2.52 0.00 0.00 4.17
2839 5404 7.519032 AAAGGAAGGTGATAAAATCGTGAAA 57.481 32.000 0.00 0.00 0.00 2.69
2957 5522 1.376037 GAGCCCTCCACCAAGTTCG 60.376 63.158 0.00 0.00 0.00 3.95
3106 5675 2.627699 GGAGGTTTGAAGCATTGGTTCA 59.372 45.455 23.52 23.52 46.16 3.18
3130 5703 3.216800 TCAAGCAAGAGAAATGCACAGT 58.783 40.909 0.00 0.00 46.22 3.55
3172 5746 3.005684 GTGACTTGATTGTTTCCATGCCA 59.994 43.478 0.00 0.00 0.00 4.92
3185 5759 4.460382 GGTGTGATTTCATGGTGACTTGAT 59.540 41.667 0.00 0.00 43.21 2.57
3189 5763 3.795688 AGGTGTGATTTCATGGTGACT 57.204 42.857 0.00 0.00 0.00 3.41
3229 5803 1.612726 GGCCTGCATCTCAGAACTGTT 60.613 52.381 0.00 0.00 45.72 3.16
3314 5888 4.825422 TCCAGTCTTATTGCTCAGAAGTG 58.175 43.478 0.00 0.00 0.00 3.16
3340 5914 2.298729 GAGGTGCTTGTTTTTATGCCCA 59.701 45.455 0.00 0.00 0.00 5.36
3362 5937 4.478317 TCCCAGTTCCACCAATAAGATGAT 59.522 41.667 0.00 0.00 0.00 2.45
3365 5940 4.325344 CCTTCCCAGTTCCACCAATAAGAT 60.325 45.833 0.00 0.00 0.00 2.40
3418 5996 4.672409 GCTTCACCGGAAAAATATTCAGG 58.328 43.478 9.46 5.93 39.26 3.86
3426 6004 1.098712 AGTGCGCTTCACCGGAAAAA 61.099 50.000 9.46 0.00 46.81 1.94
3493 6071 0.111446 TGAACTGCCGAAATGGGGAA 59.889 50.000 0.00 0.00 38.63 3.97
3537 6115 5.477984 ACCGTAGTCACTGGTAAAATCACTA 59.522 40.000 0.00 0.00 32.25 2.74
3557 6137 5.416639 AGTTTAACCAAAGAAGTTTCACCGT 59.583 36.000 0.00 0.00 0.00 4.83
3558 6138 5.886992 AGTTTAACCAAAGAAGTTTCACCG 58.113 37.500 0.00 0.00 0.00 4.94
3594 6174 7.585867 TGTGTTTTACTGCGAATATTTTGCTA 58.414 30.769 12.91 0.00 40.80 3.49
3627 6207 2.484417 CGGCGTTAGACTCCTAGTAGGA 60.484 54.545 18.15 18.15 43.43 2.94
3643 6223 0.539986 ACATATCACCCTTTCGGCGT 59.460 50.000 6.85 0.00 33.26 5.68
3645 6225 4.002906 TCATACATATCACCCTTTCGGC 57.997 45.455 0.00 0.00 33.26 5.54
3648 6228 8.908786 TTCAGATTCATACATATCACCCTTTC 57.091 34.615 0.00 0.00 0.00 2.62
3686 6269 6.536224 CAGGCAATGTAAAGGAAAATGGATTC 59.464 38.462 0.00 0.00 0.00 2.52
3740 6324 0.611896 GCACAGCTGGGGTATTGGTT 60.612 55.000 19.71 0.00 0.00 3.67
3747 6331 0.610232 GAGAAATGCACAGCTGGGGT 60.610 55.000 19.71 0.00 0.00 4.95
3765 6358 4.219507 TGTTGTTTTCTTGTTCAAGCAGGA 59.780 37.500 7.58 0.00 0.00 3.86
3803 6396 8.559536 TGTACTTCAGAACTGTGATTTTGATTC 58.440 33.333 1.73 0.00 0.00 2.52
3950 6556 0.110486 TTGCCTTCCCAGTTCCAGTC 59.890 55.000 0.00 0.00 0.00 3.51
3969 6575 6.070951 TGAAATTCTCACCTGATCATTCCT 57.929 37.500 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.