Multiple sequence alignment - TraesCS3A01G494400

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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 TraesCS3A01G494400 chr3A 100.000 3389 0 0 1 3389 720434679 720438067 0.000000e+00 6259
1 TraesCS3A01G494400 chr3A 79.872 1401 247 26 999 2377 720417148 720415761 0.000000e+00 992
2 TraesCS3A01G494400 chr3A 79.712 626 110 9 984 1596 720394162 720393541 1.440000e-118 436
3 TraesCS3A01G494400 chr3D 90.700 2785 166 43 2 2743 590366624 590369358 0.000000e+00 3622
4 TraesCS3A01G494400 chr3D 80.632 1425 243 26 964 2376 590331598 590330195 0.000000e+00 1072
5 TraesCS3A01G494400 chr3D 80.456 1402 242 21 998 2377 590356975 590355584 0.000000e+00 1042
6 TraesCS3A01G494400 chr3D 87.988 666 36 13 2748 3389 590373582 590374227 0.000000e+00 747
7 TraesCS3A01G494400 chrUn 88.968 2103 178 34 672 2749 237856446 237858519 0.000000e+00 2549
8 TraesCS3A01G494400 chrUn 88.968 2103 178 34 672 2749 297376829 297374756 0.000000e+00 2549
9 TraesCS3A01G494400 chrUn 88.968 2103 178 34 672 2749 305638085 305636012 0.000000e+00 2549
10 TraesCS3A01G494400 chrUn 86.890 656 39 12 2744 3377 237859174 237859804 0.000000e+00 691
11 TraesCS3A01G494400 chrUn 86.890 656 39 12 2744 3377 297374101 297373471 0.000000e+00 691
12 TraesCS3A01G494400 chrUn 90.726 248 21 2 2744 2990 41728585 41728339 2.520000e-86 329
13 TraesCS3A01G494400 chrUn 88.028 284 24 5 3049 3332 41727849 41727576 9.070000e-86 327
14 TraesCS3A01G494400 chrUn 88.028 284 24 5 3049 3332 41759202 41758929 9.070000e-86 327
15 TraesCS3A01G494400 chr3B 88.968 2103 178 34 672 2749 789333338 789335411 0.000000e+00 2549
16 TraesCS3A01G494400 chr3B 88.968 2103 178 34 672 2749 789368755 789370828 0.000000e+00 2549
17 TraesCS3A01G494400 chr3B 90.350 1741 155 2 960 2693 789622782 789621048 0.000000e+00 2272
18 TraesCS3A01G494400 chr3B 80.710 1436 240 23 964 2385 789324131 789322719 0.000000e+00 1083
19 TraesCS3A01G494400 chr3B 86.890 656 39 12 2744 3377 789336066 789336696 0.000000e+00 691
20 TraesCS3A01G494400 chr3B 86.890 656 39 12 2744 3377 789371483 789372113 0.000000e+00 691
21 TraesCS3A01G494400 chr3B 83.333 546 30 14 2844 3360 789612269 789611756 6.670000e-122 448
22 TraesCS3A01G494400 chr3B 81.604 212 11 7 396 586 789623283 789623079 2.110000e-32 150


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 TraesCS3A01G494400 chr3A 720434679 720438067 3388 False 6259 6259 100.000 1 3389 1 chr3A.!!$F1 3388
1 TraesCS3A01G494400 chr3A 720415761 720417148 1387 True 992 992 79.872 999 2377 1 chr3A.!!$R2 1378
2 TraesCS3A01G494400 chr3A 720393541 720394162 621 True 436 436 79.712 984 1596 1 chr3A.!!$R1 612
3 TraesCS3A01G494400 chr3D 590366624 590369358 2734 False 3622 3622 90.700 2 2743 1 chr3D.!!$F1 2741
4 TraesCS3A01G494400 chr3D 590330195 590331598 1403 True 1072 1072 80.632 964 2376 1 chr3D.!!$R1 1412
5 TraesCS3A01G494400 chr3D 590355584 590356975 1391 True 1042 1042 80.456 998 2377 1 chr3D.!!$R2 1379
6 TraesCS3A01G494400 chr3D 590373582 590374227 645 False 747 747 87.988 2748 3389 1 chr3D.!!$F2 641
7 TraesCS3A01G494400 chrUn 305636012 305638085 2073 True 2549 2549 88.968 672 2749 1 chrUn.!!$R2 2077
8 TraesCS3A01G494400 chrUn 237856446 237859804 3358 False 1620 2549 87.929 672 3377 2 chrUn.!!$F1 2705
9 TraesCS3A01G494400 chrUn 297373471 297376829 3358 True 1620 2549 87.929 672 3377 2 chrUn.!!$R4 2705
10 TraesCS3A01G494400 chrUn 41727576 41728585 1009 True 328 329 89.377 2744 3332 2 chrUn.!!$R3 588
11 TraesCS3A01G494400 chr3B 789333338 789336696 3358 False 1620 2549 87.929 672 3377 2 chr3B.!!$F1 2705
12 TraesCS3A01G494400 chr3B 789368755 789372113 3358 False 1620 2549 87.929 672 3377 2 chr3B.!!$F2 2705
13 TraesCS3A01G494400 chr3B 789621048 789623283 2235 True 1211 2272 85.977 396 2693 2 chr3B.!!$R3 2297
14 TraesCS3A01G494400 chr3B 789322719 789324131 1412 True 1083 1083 80.710 964 2385 1 chr3B.!!$R1 1421
15 TraesCS3A01G494400 chr3B 789611756 789612269 513 True 448 448 83.333 2844 3360 1 chr3B.!!$R2 516

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
660 683 0.322816 ACCGTCTACTACCTCCGCAA 60.323 55.0 0.0 0.0 0.0 4.85 F
661 684 0.381089 CCGTCTACTACCTCCGCAAG 59.619 60.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2289 2396 0.893727 CAACGGCTAGCCAAGGGTTT 60.894 55.000 32.47 12.39 35.37 3.27 R
2647 2768 1.532868 CGAGTCTGCCCAGAAAACTTG 59.467 52.381 0.00 0.00 39.48 3.16 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
42 43 6.837048 ACCCAACATTAGTTTTTGTCCTTAGT 59.163 34.615 0.00 0.00 35.28 2.24
62 63 3.770388 AGTTTAGAGCTGGTAGGAGGAAC 59.230 47.826 0.00 0.00 0.00 3.62
67 69 4.362677 AGAGCTGGTAGGAGGAACAAATA 58.637 43.478 0.00 0.00 0.00 1.40
116 118 3.466836 TGTGGCTGTAAGTTCTGAGTTG 58.533 45.455 0.00 0.00 35.30 3.16
126 128 4.000331 AGTTCTGAGTTGTGAGACCATG 58.000 45.455 0.00 0.00 0.00 3.66
131 133 2.029380 TGAGTTGTGAGACCATGTACGG 60.029 50.000 0.00 0.00 0.00 4.02
201 203 5.927954 ATAAATTTGGCAAACTTGTGCAG 57.072 34.783 16.00 0.00 46.81 4.41
265 267 5.113383 TGTTGAGACGTACTGAAAACATGT 58.887 37.500 0.00 0.00 0.00 3.21
531 554 6.754702 TTCTAGCTAGCTTTCGTTTCTCTA 57.245 37.500 24.88 0.00 0.00 2.43
598 621 2.771943 TCCCTTCGTATCCAAATCAGCT 59.228 45.455 0.00 0.00 0.00 4.24
620 643 2.962421 CAACTACCTCCTCTCATCTCCC 59.038 54.545 0.00 0.00 0.00 4.30
641 664 2.276116 ACGCGCTCTTTCTCCCTCA 61.276 57.895 5.73 0.00 0.00 3.86
648 671 2.724454 CTCTTTCTCCCTCACCGTCTA 58.276 52.381 0.00 0.00 0.00 2.59
650 673 2.041350 TCTTTCTCCCTCACCGTCTACT 59.959 50.000 0.00 0.00 0.00 2.57
656 679 1.677942 CCTCACCGTCTACTACCTCC 58.322 60.000 0.00 0.00 0.00 4.30
657 680 1.297664 CTCACCGTCTACTACCTCCG 58.702 60.000 0.00 0.00 0.00 4.63
658 681 0.745845 TCACCGTCTACTACCTCCGC 60.746 60.000 0.00 0.00 0.00 5.54
660 683 0.322816 ACCGTCTACTACCTCCGCAA 60.323 55.000 0.00 0.00 0.00 4.85
661 684 0.381089 CCGTCTACTACCTCCGCAAG 59.619 60.000 0.00 0.00 0.00 4.01
745 777 3.412386 GGCTACAAACTCTGGAACACAT 58.588 45.455 0.00 0.00 0.00 3.21
746 778 4.575885 GGCTACAAACTCTGGAACACATA 58.424 43.478 0.00 0.00 0.00 2.29
747 779 4.392138 GGCTACAAACTCTGGAACACATAC 59.608 45.833 0.00 0.00 0.00 2.39
748 780 4.994852 GCTACAAACTCTGGAACACATACA 59.005 41.667 0.00 0.00 0.00 2.29
749 781 5.468746 GCTACAAACTCTGGAACACATACAA 59.531 40.000 0.00 0.00 0.00 2.41
750 782 5.751243 ACAAACTCTGGAACACATACAAC 57.249 39.130 0.00 0.00 0.00 3.32
751 783 5.189928 ACAAACTCTGGAACACATACAACA 58.810 37.500 0.00 0.00 0.00 3.33
752 784 5.827797 ACAAACTCTGGAACACATACAACAT 59.172 36.000 0.00 0.00 0.00 2.71
753 785 5.947228 AACTCTGGAACACATACAACATG 57.053 39.130 0.00 0.00 0.00 3.21
756 788 3.073798 TCTGGAACACATACAACATGGGT 59.926 43.478 0.00 0.00 37.23 4.51
772 804 1.002011 GGTTGGGGACTTGAGAGGC 60.002 63.158 0.00 0.00 0.00 4.70
786 818 1.408702 GAGAGGCTAGCTCAACTCCAG 59.591 57.143 15.72 0.00 32.67 3.86
810 848 0.731417 GCAACTGCATGCTACTCTGG 59.269 55.000 20.33 3.25 43.06 3.86
814 852 2.739943 ACTGCATGCTACTCTGGTAGA 58.260 47.619 20.33 0.00 46.01 2.59
866 904 3.683365 ATGGATCAAAAAGGTGCCAAC 57.317 42.857 0.00 0.00 0.00 3.77
868 906 2.971330 TGGATCAAAAAGGTGCCAACAT 59.029 40.909 0.00 0.00 0.00 2.71
871 909 5.070981 TGGATCAAAAAGGTGCCAACATAAA 59.929 36.000 0.00 0.00 0.00 1.40
896 934 4.903045 TCCTCCCGTCTGTTCTATTTTT 57.097 40.909 0.00 0.00 0.00 1.94
957 1001 9.162764 TGCTTGAAAGATTATACTCTGTTTACC 57.837 33.333 0.00 0.00 0.00 2.85
958 1002 8.328864 GCTTGAAAGATTATACTCTGTTTACCG 58.671 37.037 0.00 0.00 0.00 4.02
1009 1090 1.407936 CGTCCTGGAGATGGATCAGT 58.592 55.000 0.00 0.00 35.87 3.41
1066 1147 2.825836 CATCCAAGGCGCAGGTCC 60.826 66.667 10.83 0.00 0.00 4.46
1067 1148 3.011517 ATCCAAGGCGCAGGTCCT 61.012 61.111 10.83 0.00 34.90 3.85
1160 1244 0.391528 TACGATCCTGACCACGTCGA 60.392 55.000 0.00 0.00 39.59 4.20
1233 1317 2.358003 GAGCACGACAAGCTGGCT 60.358 61.111 0.00 0.00 43.58 4.75
1363 1453 3.612241 CGCCAACACATTTGATGACATGT 60.612 43.478 0.00 0.00 0.00 3.21
1556 1659 1.027357 GCGGAGAACCAGATACCGTA 58.973 55.000 0.00 0.00 44.48 4.02
1623 1726 3.257375 AGGAACGTGTGCTTACAGACATA 59.743 43.478 0.00 0.00 40.01 2.29
1627 1730 4.816392 ACGTGTGCTTACAGACATATCAA 58.184 39.130 0.00 0.00 40.01 2.57
1755 1861 1.027357 ACTTGAAGCCTGTTGCACTG 58.973 50.000 0.00 0.00 44.83 3.66
2139 2245 1.444119 GCAACAACGAAGAGGTGGCA 61.444 55.000 0.00 0.00 43.31 4.92
2241 2347 2.035442 GCTGGAGAAGCGGTTCCAC 61.035 63.158 22.91 16.28 43.45 4.02
2289 2396 3.195825 GGCTAAAGCAGAGGTACTTGAGA 59.804 47.826 4.07 0.00 41.16 3.27
2418 2525 9.788960 AATTAGAAATCTAAACATCTTTTCGGC 57.211 29.630 6.95 0.00 41.27 5.54
2419 2526 8.561738 TTAGAAATCTAAACATCTTTTCGGCT 57.438 30.769 0.44 0.00 35.67 5.52
2421 2528 7.886338 AGAAATCTAAACATCTTTTCGGCTTT 58.114 30.769 0.00 0.00 32.84 3.51
2426 2533 7.590279 TCTAAACATCTTTTCGGCTTTTAAGG 58.410 34.615 0.00 0.00 0.00 2.69
2429 2536 5.070685 ACATCTTTTCGGCTTTTAAGGACT 58.929 37.500 0.00 0.00 0.00 3.85
2449 2556 5.855395 GGACTGGACGTCACGATAATAATAC 59.145 44.000 18.91 0.00 44.68 1.89
2533 2641 6.441274 GCCATCACACTTATGGAATGTATTG 58.559 40.000 6.29 0.00 45.77 1.90
2567 2682 8.931775 TGTATTATGTGTTGTGAGTTATGACAC 58.068 33.333 0.00 0.00 40.62 3.67
2575 2690 5.441709 TGTGAGTTATGACACGTTCACTA 57.558 39.130 12.45 0.00 36.92 2.74
2607 2722 4.584638 AGGGCTGTTGGACAATGTATAA 57.415 40.909 0.00 0.00 0.00 0.98
2664 2785 2.297701 TGACAAGTTTTCTGGGCAGAC 58.702 47.619 0.00 0.00 33.15 3.51
2665 2786 2.092429 TGACAAGTTTTCTGGGCAGACT 60.092 45.455 0.00 0.00 33.15 3.24
2684 2805 6.385843 CAGACTCGATCTATTTGAGGTATGG 58.614 44.000 0.00 0.00 39.84 2.74
2695 2816 3.439857 TGAGGTATGGCTTTGCTCTTT 57.560 42.857 0.00 0.00 0.00 2.52
2696 2817 3.084039 TGAGGTATGGCTTTGCTCTTTG 58.916 45.455 0.00 0.00 0.00 2.77
2729 2850 2.226330 TCAGTGTGTATTGGTGTTGGC 58.774 47.619 0.00 0.00 0.00 4.52
2746 3526 1.211703 TGGCTGCATAAATCGAAGGGA 59.788 47.619 0.50 0.00 0.00 4.20
2822 3602 3.701542 TCTAGATTGGGTGTACAGAGCTG 59.298 47.826 0.00 0.00 0.00 4.24
2880 3661 2.581216 TTTGCGGGGTATTGGTGTTA 57.419 45.000 0.00 0.00 0.00 2.41
2990 3772 6.695429 TGAGGATAAGAATGGAAGATGATCG 58.305 40.000 0.00 0.00 0.00 3.69
2991 3773 6.268617 TGAGGATAAGAATGGAAGATGATCGT 59.731 38.462 0.00 0.00 0.00 3.73
2992 3774 6.462500 AGGATAAGAATGGAAGATGATCGTG 58.538 40.000 0.00 0.00 0.00 4.35
2993 3775 5.121454 GGATAAGAATGGAAGATGATCGTGC 59.879 44.000 0.00 0.00 0.00 5.34
2994 3776 3.548745 AGAATGGAAGATGATCGTGCA 57.451 42.857 4.99 4.99 30.58 4.57
2995 3777 4.082665 AGAATGGAAGATGATCGTGCAT 57.917 40.909 9.31 9.31 38.38 3.96
2996 3778 3.813724 AGAATGGAAGATGATCGTGCATG 59.186 43.478 15.00 0.00 37.07 4.06
2997 3779 1.302366 TGGAAGATGATCGTGCATGC 58.698 50.000 11.82 11.82 0.00 4.06
2998 3780 1.302366 GGAAGATGATCGTGCATGCA 58.698 50.000 18.46 18.46 0.00 3.96
2999 3781 1.003116 GGAAGATGATCGTGCATGCAC 60.003 52.381 35.76 35.76 43.01 4.57
3093 4325 4.403585 TCTCCTCTCATGCATCTTTCTG 57.596 45.455 0.00 0.00 0.00 3.02
3161 4393 1.813513 GTGGCTGCAAGAAAGCTAGA 58.186 50.000 0.50 0.00 40.64 2.43
3165 4397 3.452264 TGGCTGCAAGAAAGCTAGATAGA 59.548 43.478 0.50 0.00 40.64 1.98
3167 4399 4.511082 GGCTGCAAGAAAGCTAGATAGAAG 59.489 45.833 0.50 0.00 40.64 2.85
3170 4402 6.093357 GCTGCAAGAAAGCTAGATAGAAGTTT 59.907 38.462 0.00 0.00 37.69 2.66
3182 4414 6.325919 AGATAGAAGTTTCGCCTGATAGAG 57.674 41.667 0.00 0.00 0.00 2.43
3205 4437 2.365293 GGTTTGGCCTGACTTGATTGTT 59.635 45.455 3.32 0.00 0.00 2.83
3231 4463 2.045926 GTTCCCTGCCTGCATCGT 60.046 61.111 0.00 0.00 0.00 3.73
3288 4520 1.021202 TGGCAACGAAACTGTCAAGG 58.979 50.000 0.00 0.00 42.51 3.61
3315 4547 0.112995 TGGTCCATCTTGCTGCCTTT 59.887 50.000 0.00 0.00 0.00 3.11
3318 4550 1.138247 CCATCTTGCTGCCTTTCGC 59.862 57.895 0.00 0.00 38.31 4.70
3320 4552 3.044059 ATCTTGCTGCCTTTCGCGC 62.044 57.895 0.00 0.00 42.08 6.86
3365 4597 7.549134 TGGAATACATGCTTTTAGTGTCAGTAG 59.451 37.037 0.00 0.00 0.00 2.57
3385 4617 3.104512 AGGTATCAAACTCCATCCGTGA 58.895 45.455 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.989131 ACTAATGTTGGGTAACTCTACACATAT 58.011 33.333 0.00 0.00 41.15 1.78
4 5 8.370266 ACTAATGTTGGGTAACTCTACACATA 57.630 34.615 0.00 0.00 41.15 2.29
5 6 7.253905 ACTAATGTTGGGTAACTCTACACAT 57.746 36.000 0.00 0.00 41.15 3.21
6 7 6.675413 ACTAATGTTGGGTAACTCTACACA 57.325 37.500 0.00 0.00 39.77 3.72
7 8 7.974482 AAACTAATGTTGGGTAACTCTACAC 57.026 36.000 0.00 0.00 37.68 2.90
42 43 3.786553 TGTTCCTCCTACCAGCTCTAAA 58.213 45.455 0.00 0.00 0.00 1.85
100 102 4.985409 GGTCTCACAACTCAGAACTTACAG 59.015 45.833 0.00 0.00 0.00 2.74
104 106 4.141620 ACATGGTCTCACAACTCAGAACTT 60.142 41.667 0.00 0.00 0.00 2.66
110 112 2.029380 CCGTACATGGTCTCACAACTCA 60.029 50.000 0.00 0.00 0.00 3.41
116 118 0.175073 GGGTCCGTACATGGTCTCAC 59.825 60.000 0.00 0.00 0.00 3.51
126 128 3.318557 CCTCTCTAAATCTGGGTCCGTAC 59.681 52.174 0.00 0.00 0.00 3.67
131 133 1.418264 GGGCCTCTCTAAATCTGGGTC 59.582 57.143 0.84 0.00 0.00 4.46
265 267 1.459450 GCCAGCGGTTTGGAATAGAA 58.541 50.000 5.08 0.00 40.87 2.10
340 342 1.045407 TTAGGCAGTCGTGTGAGGTT 58.955 50.000 0.00 0.00 0.00 3.50
341 343 1.000955 CTTTAGGCAGTCGTGTGAGGT 59.999 52.381 0.00 0.00 0.00 3.85
342 344 1.000955 ACTTTAGGCAGTCGTGTGAGG 59.999 52.381 0.00 0.00 0.00 3.86
428 432 2.054140 TTGGCGTGACCGTTGCTTTC 62.054 55.000 0.00 0.00 43.94 2.62
531 554 6.875726 GGTAGTAACGTTTTACCCAAAGAGAT 59.124 38.462 21.94 0.00 38.79 2.75
598 621 3.373220 GGGAGATGAGAGGAGGTAGTTGA 60.373 52.174 0.00 0.00 0.00 3.18
620 643 1.807573 GGGAGAAAGAGCGCGTGAG 60.808 63.158 8.43 0.00 0.00 3.51
641 664 0.322816 TTGCGGAGGTAGTAGACGGT 60.323 55.000 0.00 0.00 0.00 4.83
688 716 1.961378 CAGCAAGACCAGCATGCAA 59.039 52.632 21.98 0.00 43.38 4.08
748 780 0.856982 TCAAGTCCCCAACCCATGTT 59.143 50.000 0.00 0.00 34.14 2.71
749 781 0.405585 CTCAAGTCCCCAACCCATGT 59.594 55.000 0.00 0.00 0.00 3.21
750 782 0.698238 TCTCAAGTCCCCAACCCATG 59.302 55.000 0.00 0.00 0.00 3.66
751 783 0.995024 CTCTCAAGTCCCCAACCCAT 59.005 55.000 0.00 0.00 0.00 4.00
752 784 1.133809 CCTCTCAAGTCCCCAACCCA 61.134 60.000 0.00 0.00 0.00 4.51
753 785 1.685820 CCTCTCAAGTCCCCAACCC 59.314 63.158 0.00 0.00 0.00 4.11
756 788 1.573108 CTAGCCTCTCAAGTCCCCAA 58.427 55.000 0.00 0.00 0.00 4.12
760 792 1.479709 TGAGCTAGCCTCTCAAGTCC 58.520 55.000 12.13 0.00 41.35 3.85
810 848 1.877165 GCCTTACGCTGCCGTCTAC 60.877 63.158 0.00 0.00 46.39 2.59
833 871 3.159213 TGATCCATTTGCTTGTCCACT 57.841 42.857 0.00 0.00 0.00 4.00
866 904 6.525629 AGAACAGACGGGAGGATAATTTATG 58.474 40.000 0.00 0.00 0.00 1.90
868 906 7.850935 ATAGAACAGACGGGAGGATAATTTA 57.149 36.000 0.00 0.00 0.00 1.40
871 909 6.749036 AAATAGAACAGACGGGAGGATAAT 57.251 37.500 0.00 0.00 0.00 1.28
932 976 8.328864 CGGTAAACAGAGTATAATCTTTCAAGC 58.671 37.037 0.00 0.00 0.00 4.01
933 977 9.582431 TCGGTAAACAGAGTATAATCTTTCAAG 57.418 33.333 0.00 0.00 0.00 3.02
940 984 7.541437 GCCTACATCGGTAAACAGAGTATAATC 59.459 40.741 0.00 0.00 0.00 1.75
945 989 3.382546 GGCCTACATCGGTAAACAGAGTA 59.617 47.826 0.00 0.00 0.00 2.59
957 1001 1.611977 TCCGTAGATTGGCCTACATCG 59.388 52.381 3.32 2.01 39.08 3.84
958 1002 3.963428 ATCCGTAGATTGGCCTACATC 57.037 47.619 3.32 2.97 39.08 3.06
1122 1206 2.428569 TCGCTGCTGTCGACGTTC 60.429 61.111 11.62 2.83 0.00 3.95
1160 1244 0.174162 GTAGTTGTACGGGCCGATGT 59.826 55.000 35.78 13.66 0.00 3.06
1213 1297 2.320587 CCAGCTTGTCGTGCTCCAC 61.321 63.158 0.00 0.00 38.92 4.02
1233 1317 2.037367 AGCACCAGGTCGAGGCTA 59.963 61.111 0.13 0.00 32.09 3.93
1297 1387 2.119655 GGCATGCCAGCTCCTTGAG 61.120 63.158 32.08 0.00 35.81 3.02
1323 1413 0.670546 CGTAGCAGTTCCTGGTGTGG 60.671 60.000 6.22 0.00 42.42 4.17
1605 1708 4.450082 TGATATGTCTGTAAGCACACGT 57.550 40.909 0.00 0.00 29.33 4.49
1627 1730 8.712103 TCTCCTCATGAGATCAAGTGAATAATT 58.288 33.333 24.62 0.00 45.29 1.40
1755 1861 4.148825 ATGGCAGGCGAGACGGAC 62.149 66.667 0.00 0.00 0.00 4.79
2241 2347 4.514577 CACCTCCGCGGGTAGCTG 62.515 72.222 27.83 10.12 45.59 4.24
2289 2396 0.893727 CAACGGCTAGCCAAGGGTTT 60.894 55.000 32.47 12.39 35.37 3.27
2429 2536 8.382030 TCTAAGTATTATTATCGTGACGTCCA 57.618 34.615 14.12 0.00 0.00 4.02
2449 2556 5.759506 AGTCACGTAGGACATGATCTAAG 57.240 43.478 0.00 5.68 40.29 2.18
2533 2641 9.151471 ACTCACAACACATAATACATGACTAAC 57.849 33.333 0.00 0.00 0.00 2.34
2567 2682 3.512680 CCTTAAGGCTGTCTAGTGAACG 58.487 50.000 9.00 0.00 0.00 3.95
2636 2751 5.406477 GCCCAGAAAACTTGTCATCATTTTC 59.594 40.000 0.00 0.00 40.01 2.29
2647 2768 1.532868 CGAGTCTGCCCAGAAAACTTG 59.467 52.381 0.00 0.00 39.48 3.16
2653 2774 2.437085 TAGATCGAGTCTGCCCAGAA 57.563 50.000 0.00 0.00 39.48 3.02
2664 2785 5.398603 AGCCATACCTCAAATAGATCGAG 57.601 43.478 0.00 0.00 0.00 4.04
2665 2786 5.808366 AAGCCATACCTCAAATAGATCGA 57.192 39.130 0.00 0.00 0.00 3.59
2684 2805 0.249031 ACGCCAACAAAGAGCAAAGC 60.249 50.000 0.00 0.00 0.00 3.51
2695 2816 1.270785 ACACTGATGATCACGCCAACA 60.271 47.619 0.00 0.00 0.00 3.33
2696 2817 1.129251 CACACTGATGATCACGCCAAC 59.871 52.381 0.00 0.00 0.00 3.77
2729 2850 3.879295 ACACATCCCTTCGATTTATGCAG 59.121 43.478 0.00 0.00 0.00 4.41
2746 3526 5.095145 AGATGAGTGCAATGAGTACACAT 57.905 39.130 0.00 0.00 44.13 3.21
2926 3707 7.726033 AGAGGATGGGTTATATACACAGATC 57.274 40.000 0.00 0.00 45.06 2.75
2978 3760 1.302366 GCATGCACGATCATCTTCCA 58.698 50.000 14.21 0.00 0.00 3.53
2990 3772 2.747436 TCTATCAGATCGTGCATGCAC 58.253 47.619 35.76 35.76 43.01 4.57
2991 3773 3.672767 ATCTATCAGATCGTGCATGCA 57.327 42.857 18.46 18.46 25.75 3.96
2992 3774 4.925646 TGTAATCTATCAGATCGTGCATGC 59.074 41.667 11.82 11.82 32.89 4.06
2993 3775 5.922544 TGTGTAATCTATCAGATCGTGCATG 59.077 40.000 0.00 0.00 32.89 4.06
2994 3776 6.089249 TGTGTAATCTATCAGATCGTGCAT 57.911 37.500 0.00 0.00 32.89 3.96
2995 3777 5.507985 CCTGTGTAATCTATCAGATCGTGCA 60.508 44.000 0.00 0.00 32.89 4.57
2996 3778 4.920340 CCTGTGTAATCTATCAGATCGTGC 59.080 45.833 0.00 0.00 32.89 5.34
2997 3779 6.319141 TCCTGTGTAATCTATCAGATCGTG 57.681 41.667 0.00 0.00 32.89 4.35
2998 3780 6.515862 GCTTCCTGTGTAATCTATCAGATCGT 60.516 42.308 0.00 0.00 32.89 3.73
2999 3781 5.861251 GCTTCCTGTGTAATCTATCAGATCG 59.139 44.000 0.00 0.00 32.89 3.69
3000 3782 6.867816 CAGCTTCCTGTGTAATCTATCAGATC 59.132 42.308 0.00 0.00 32.25 2.75
3001 3783 6.740960 GCAGCTTCCTGTGTAATCTATCAGAT 60.741 42.308 0.00 0.00 41.26 2.90
3002 3784 5.452496 GCAGCTTCCTGTGTAATCTATCAGA 60.452 44.000 0.00 0.00 41.26 3.27
3003 3785 4.749099 GCAGCTTCCTGTGTAATCTATCAG 59.251 45.833 0.00 0.00 41.26 2.90
3131 4363 2.844451 GCAGCCACGCAACCTTTCA 61.844 57.895 0.00 0.00 0.00 2.69
3161 4393 5.221342 CCACTCTATCAGGCGAAACTTCTAT 60.221 44.000 0.00 0.00 0.00 1.98
3165 4397 2.567615 ACCACTCTATCAGGCGAAACTT 59.432 45.455 0.00 0.00 0.00 2.66
3167 4399 2.674796 ACCACTCTATCAGGCGAAAC 57.325 50.000 0.00 0.00 0.00 2.78
3170 4402 1.207089 CCAAACCACTCTATCAGGCGA 59.793 52.381 0.00 0.00 0.00 5.54
3182 4414 1.620822 ATCAAGTCAGGCCAAACCAC 58.379 50.000 5.01 0.00 43.14 4.16
3231 4463 3.920231 AGCATCCAAGTAGCTTGATGA 57.080 42.857 10.12 1.25 43.42 2.92
3288 4520 3.066342 CAGCAAGATGGACCATGAATGAC 59.934 47.826 12.99 0.00 0.00 3.06
3320 4552 1.396996 CAAACTATTGGACGGAAGCCG 59.603 52.381 4.03 4.03 41.87 5.52
3333 4565 9.243105 ACACTAAAAGCATGTATTCCAAACTAT 57.757 29.630 0.00 0.00 0.00 2.12
3334 4566 8.630054 ACACTAAAAGCATGTATTCCAAACTA 57.370 30.769 0.00 0.00 0.00 2.24
3365 4597 3.195661 GTCACGGATGGAGTTTGATACC 58.804 50.000 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.