Multiple sequence alignment - TraesCS2D01G322800

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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 TraesCS2D01G322800 chr2D 100.000 6528 0 0 1 6528 414408423 414401896 0.000000e+00 12056
1 TraesCS2D01G322800 chr2D 88.853 619 67 2 2 618 88122042 88122660 0.000000e+00 760
2 TraesCS2D01G322800 chr2A 95.307 5945 201 37 617 6528 581583463 581577564 0.000000e+00 9361
3 TraesCS2D01G322800 chr2B 96.492 3421 96 10 3103 6518 488012729 488009328 0.000000e+00 5631
4 TraesCS2D01G322800 chr2B 94.329 2451 83 14 669 3105 488020730 488018322 0.000000e+00 3705
5 TraesCS2D01G322800 chr2B 88.493 617 65 5 2 615 677800472 677801085 0.000000e+00 741
6 TraesCS2D01G322800 chr3B 88.961 616 65 3 2 615 513714282 513714896 0.000000e+00 758
7 TraesCS2D01G322800 chr3D 88.376 628 69 4 2 626 338583619 338582993 0.000000e+00 752
8 TraesCS2D01G322800 chr3D 87.200 625 69 10 1 619 447615872 447616491 0.000000e+00 701
9 TraesCS2D01G322800 chr3D 85.852 622 82 6 1 619 496509299 496508681 0.000000e+00 656
10 TraesCS2D01G322800 chr5D 88.762 614 65 3 2 615 35322277 35322886 0.000000e+00 749
11 TraesCS2D01G322800 chr5D 92.060 403 32 0 6036 6438 513978963 513978561 9.500000e-158 568
12 TraesCS2D01G322800 chr7D 88.350 618 71 1 1 617 607078696 607079313 0.000000e+00 741
13 TraesCS2D01G322800 chr7D 88.488 582 63 4 34 614 426868471 426869049 0.000000e+00 701
14 TraesCS2D01G322800 chr5A 92.079 404 32 0 6036 6439 641733852 641733449 2.640000e-158 569
15 TraesCS2D01G322800 chr5B 91.832 404 33 0 6036 6439 644890469 644890066 1.230000e-156 564
16 TraesCS2D01G322800 chr4B 81.159 276 46 6 3242 3514 646273981 646274253 3.960000e-52 217
17 TraesCS2D01G322800 chr4B 81.159 276 46 5 3242 3514 646307552 646307824 3.960000e-52 217
18 TraesCS2D01G322800 chr4B 80.866 277 44 8 3242 3514 646360799 646361070 6.630000e-50 209
19 TraesCS2D01G322800 chr4B 80.435 276 48 6 3242 3514 646333506 646333778 8.580000e-49 206
20 TraesCS2D01G322800 chrUn 83.010 206 32 3 3309 3514 478128764 478128562 4.020000e-42 183
21 TraesCS2D01G322800 chr6B 82.258 186 29 3 6039 6224 39324667 39324848 2.440000e-34 158


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 TraesCS2D01G322800 chr2D 414401896 414408423 6527 True 12056 12056 100.000 1 6528 1 chr2D.!!$R1 6527
1 TraesCS2D01G322800 chr2D 88122042 88122660 618 False 760 760 88.853 2 618 1 chr2D.!!$F1 616
2 TraesCS2D01G322800 chr2A 581577564 581583463 5899 True 9361 9361 95.307 617 6528 1 chr2A.!!$R1 5911
3 TraesCS2D01G322800 chr2B 488009328 488012729 3401 True 5631 5631 96.492 3103 6518 1 chr2B.!!$R1 3415
4 TraesCS2D01G322800 chr2B 488018322 488020730 2408 True 3705 3705 94.329 669 3105 1 chr2B.!!$R2 2436
5 TraesCS2D01G322800 chr2B 677800472 677801085 613 False 741 741 88.493 2 615 1 chr2B.!!$F1 613
6 TraesCS2D01G322800 chr3B 513714282 513714896 614 False 758 758 88.961 2 615 1 chr3B.!!$F1 613
7 TraesCS2D01G322800 chr3D 338582993 338583619 626 True 752 752 88.376 2 626 1 chr3D.!!$R1 624
8 TraesCS2D01G322800 chr3D 447615872 447616491 619 False 701 701 87.200 1 619 1 chr3D.!!$F1 618
9 TraesCS2D01G322800 chr3D 496508681 496509299 618 True 656 656 85.852 1 619 1 chr3D.!!$R2 618
10 TraesCS2D01G322800 chr5D 35322277 35322886 609 False 749 749 88.762 2 615 1 chr5D.!!$F1 613
11 TraesCS2D01G322800 chr7D 607078696 607079313 617 False 741 741 88.350 1 617 1 chr7D.!!$F2 616
12 TraesCS2D01G322800 chr7D 426868471 426869049 578 False 701 701 88.488 34 614 1 chr7D.!!$F1 580

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
181 182 0.109365 GCAATGTGGTTATGTGCGCA 60.109 50.000 5.66 5.66 0.00 6.09 F
540 542 0.243907 CGTCTTCGAGTGTCCCACAT 59.756 55.000 0.00 0.00 39.71 3.21 F
608 611 0.316442 CACGTGCTTTGTGTGCTCTG 60.316 55.000 0.82 0.00 32.68 3.35 F
1409 1431 1.338200 CCTCTCGGTCTGACCCTTTTG 60.338 57.143 20.68 6.79 33.75 2.44 F
2399 2425 1.251251 ATTGCAACCTCCAAGCTGAC 58.749 50.000 0.00 0.00 0.00 3.51 F
2686 2714 1.898472 TGAGGTTGAAGCTCTCAGAGG 59.102 52.381 22.93 0.00 42.83 3.69 F
2933 2969 4.218852 ACTTGTTCAAACCAAACCGAGAAA 59.781 37.500 0.00 0.00 0.00 2.52 F
4495 4535 4.462483 AGGTTGACTTGAAGTTCTTTTGCA 59.538 37.500 0.00 0.00 0.00 4.08 F
5380 5421 0.325933 CATGCTTGGGTGGAGACTCA 59.674 55.000 4.53 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1577 1601 0.116342 TAGAGGCAGGACCAGAACCA 59.884 55.000 0.00 0.00 43.14 3.67 R
1578 1602 1.066071 GTTAGAGGCAGGACCAGAACC 60.066 57.143 0.00 0.00 43.14 3.62 R
1806 1832 1.575244 TGTCTGCAGCATCGATTAGC 58.425 50.000 9.47 0.00 0.00 3.09 R
2665 2693 2.353605 CCTCTGAGAGCTTCAACCTCAC 60.354 54.545 6.17 0.00 34.81 3.51 R
3881 3920 5.764686 AGATGAAGTGCACAGTGATTAACAA 59.235 36.000 21.04 0.00 0.00 2.83 R
4435 4475 4.271049 CGTTTGAGCAGAGAAGAAACTTCA 59.729 41.667 12.86 0.00 0.00 3.02 R
4705 4745 4.799564 CTCTTTGGAGAGTTAGCTGAGT 57.200 45.455 0.00 0.00 43.66 3.41 R
5402 5443 0.037232 GAAGACACTTCCGGGGACAG 60.037 60.000 0.00 0.00 0.00 3.51 R
6195 6284 1.227089 GCTCATCACCGCGACAGAT 60.227 57.895 8.23 4.71 0.00 2.90 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
61 62 1.133253 CTTGCCTCACAACATCGCG 59.867 57.895 0.00 0.00 33.68 5.87
69 70 1.227409 ACAACATCGCGTGTGGACA 60.227 52.632 18.84 0.00 41.14 4.02
123 124 3.391382 ACCTCGGCCTGCTACACC 61.391 66.667 0.00 0.00 0.00 4.16
144 145 1.004277 GTCTGCAGGACGAAGACACG 61.004 60.000 15.13 0.00 40.08 4.49
181 182 0.109365 GCAATGTGGTTATGTGCGCA 60.109 50.000 5.66 5.66 0.00 6.09
261 262 1.909302 GACTCCTTCCTGGAATGGTGA 59.091 52.381 22.42 12.62 45.63 4.02
298 299 1.464997 GCTTCGCGAAGGAAGACAAAT 59.535 47.619 40.64 0.00 44.93 2.32
323 324 4.351407 TGGTTTTGACACCCTGGTTATCTA 59.649 41.667 0.00 0.00 35.73 1.98
324 325 5.163077 TGGTTTTGACACCCTGGTTATCTAA 60.163 40.000 0.00 0.00 35.73 2.10
493 494 5.482908 GCTTTGTGAGAGATTAGTCTTGGA 58.517 41.667 0.00 0.00 33.97 3.53
521 523 1.228154 GGAGTGGTGGTGGGTGTTC 60.228 63.158 0.00 0.00 0.00 3.18
540 542 0.243907 CGTCTTCGAGTGTCCCACAT 59.756 55.000 0.00 0.00 39.71 3.21
544 546 2.104111 TCTTCGAGTGTCCCACATTTGT 59.896 45.455 0.00 0.00 36.74 2.83
608 611 0.316442 CACGTGCTTTGTGTGCTCTG 60.316 55.000 0.82 0.00 32.68 3.35
693 696 2.662070 GGCCGGCCCAGTACTGTAA 61.662 63.158 36.64 0.00 0.00 2.41
782 796 2.159226 CCCGCTCGTTCTACTCATCTTT 60.159 50.000 0.00 0.00 0.00 2.52
783 797 3.109619 CCGCTCGTTCTACTCATCTTTC 58.890 50.000 0.00 0.00 0.00 2.62
784 798 3.181495 CCGCTCGTTCTACTCATCTTTCT 60.181 47.826 0.00 0.00 0.00 2.52
785 799 4.416620 CGCTCGTTCTACTCATCTTTCTT 58.583 43.478 0.00 0.00 0.00 2.52
786 800 4.497608 CGCTCGTTCTACTCATCTTTCTTC 59.502 45.833 0.00 0.00 0.00 2.87
787 801 5.646606 GCTCGTTCTACTCATCTTTCTTCT 58.353 41.667 0.00 0.00 0.00 2.85
788 802 5.741982 GCTCGTTCTACTCATCTTTCTTCTC 59.258 44.000 0.00 0.00 0.00 2.87
789 803 6.623986 GCTCGTTCTACTCATCTTTCTTCTCA 60.624 42.308 0.00 0.00 0.00 3.27
790 804 7.215719 TCGTTCTACTCATCTTTCTTCTCAA 57.784 36.000 0.00 0.00 0.00 3.02
791 805 7.658261 TCGTTCTACTCATCTTTCTTCTCAAA 58.342 34.615 0.00 0.00 0.00 2.69
792 806 8.141909 TCGTTCTACTCATCTTTCTTCTCAAAA 58.858 33.333 0.00 0.00 0.00 2.44
793 807 8.765219 CGTTCTACTCATCTTTCTTCTCAAAAA 58.235 33.333 0.00 0.00 0.00 1.94
1286 1302 2.159653 CGCAACAGACAGCAGAAATACC 60.160 50.000 0.00 0.00 0.00 2.73
1288 1304 3.120060 GCAACAGACAGCAGAAATACCAG 60.120 47.826 0.00 0.00 0.00 4.00
1342 1360 2.749621 CCTCCTGTTTAGTGTTGCCATC 59.250 50.000 0.00 0.00 0.00 3.51
1409 1431 1.338200 CCTCTCGGTCTGACCCTTTTG 60.338 57.143 20.68 6.79 33.75 2.44
1469 1491 6.572519 AGCTTGCAAGAACAATTTAGAACAA 58.427 32.000 30.39 0.00 0.00 2.83
1496 1518 2.357637 GACTCTCTAATCTGCGCTCAGT 59.642 50.000 9.73 0.00 41.10 3.41
1572 1596 8.875803 CATAAGTGAAATTCCATGATTTTGGTG 58.124 33.333 0.00 0.00 38.01 4.17
1575 1599 7.682628 AGTGAAATTCCATGATTTTGGTGAAT 58.317 30.769 0.00 0.00 38.01 2.57
1576 1600 7.604927 AGTGAAATTCCATGATTTTGGTGAATG 59.395 33.333 0.00 0.00 38.01 2.67
1577 1601 7.388500 GTGAAATTCCATGATTTTGGTGAATGT 59.612 33.333 0.00 0.00 38.01 2.71
1578 1602 7.388224 TGAAATTCCATGATTTTGGTGAATGTG 59.612 33.333 0.00 0.00 38.01 3.21
1615 1641 5.523188 CCTCTAACATGTCTTTCTGATGAGC 59.477 44.000 0.00 0.00 0.00 4.26
1806 1832 4.737054 CTGAAATCGGAAAACTCAATGGG 58.263 43.478 0.00 0.00 0.00 4.00
1909 1935 5.290493 TGACTGTACTGACTGAATTGGTT 57.710 39.130 6.77 0.00 0.00 3.67
2058 2084 3.605634 TGTACCTTGTGCATTTCGCTAT 58.394 40.909 0.00 0.00 43.06 2.97
2063 2089 5.399013 ACCTTGTGCATTTCGCTATTTTAC 58.601 37.500 0.00 0.00 43.06 2.01
2136 2162 3.068873 AGTGCCTTCGATCTTATGGAGAC 59.931 47.826 0.00 0.00 37.17 3.36
2399 2425 1.251251 ATTGCAACCTCCAAGCTGAC 58.749 50.000 0.00 0.00 0.00 3.51
2510 2536 4.199310 ACTCAGTAAAGTTGCAGCTTGAA 58.801 39.130 17.08 5.57 0.00 2.69
2529 2555 7.765819 AGCTTGAAATGGCAAAGGTAATATTTC 59.234 33.333 0.00 0.00 35.93 2.17
2564 2592 6.804770 TTTAACTGCATTCTTTACGCCTTA 57.195 33.333 0.00 0.00 0.00 2.69
2686 2714 1.898472 TGAGGTTGAAGCTCTCAGAGG 59.102 52.381 22.93 0.00 42.83 3.69
2885 2921 7.014230 GCTAACCATTTCAATTAGGATGGCTTA 59.986 37.037 11.16 8.90 42.17 3.09
2886 2922 7.919385 AACCATTTCAATTAGGATGGCTTAT 57.081 32.000 11.16 0.00 42.17 1.73
2927 2963 4.629634 CAGGAAACTTGTTCAAACCAAACC 59.370 41.667 0.00 0.00 40.21 3.27
2933 2969 4.218852 ACTTGTTCAAACCAAACCGAGAAA 59.781 37.500 0.00 0.00 0.00 2.52
3239 3276 9.832445 TTGTAATTGTTTACTATCCAGAGATCC 57.168 33.333 0.00 0.00 38.81 3.36
3649 3687 7.725818 ACTTGCTAACTTCTGTAAACTAACC 57.274 36.000 0.00 0.00 0.00 2.85
4494 4534 4.800471 CAGGTTGACTTGAAGTTCTTTTGC 59.200 41.667 0.00 0.00 0.00 3.68
4495 4535 4.462483 AGGTTGACTTGAAGTTCTTTTGCA 59.538 37.500 0.00 0.00 0.00 4.08
4751 4792 5.163426 TGTTCAATTTGGTTGCAATGTCTCT 60.163 36.000 0.59 0.00 37.74 3.10
4850 4891 9.185192 GTAGGAAAAACACAAATGAATGAAGAG 57.815 33.333 0.00 0.00 0.00 2.85
5110 5151 5.452078 TTGCTATCCCTTTGTTTTGTGAG 57.548 39.130 0.00 0.00 0.00 3.51
5353 5394 5.473504 CAGCCTACAACTGTTTTCCTTGTAT 59.526 40.000 0.00 0.00 31.59 2.29
5357 5398 7.572539 GCCTACAACTGTTTTCCTTGTATACAC 60.573 40.741 4.68 0.00 31.59 2.90
5358 5399 7.442969 CCTACAACTGTTTTCCTTGTATACACA 59.557 37.037 4.68 0.00 31.59 3.72
5380 5421 0.325933 CATGCTTGGGTGGAGACTCA 59.674 55.000 4.53 0.00 0.00 3.41
5402 5443 4.483476 AAGACGCTAATGTTTGTGAACC 57.517 40.909 0.00 0.00 34.80 3.62
5530 5571 3.866066 GCAGCTTGTCACAAGGATGAGTA 60.866 47.826 19.35 0.00 0.00 2.59
5559 5600 3.251004 GTCAATTCACTGTCAAGTCCCAC 59.749 47.826 0.00 0.00 32.98 4.61
5845 5886 9.567848 TCAGCCTTTTATTTTATTCTAAAAGCG 57.432 29.630 8.55 4.95 40.86 4.68
6077 6166 3.008375 ACTTCCTGCAGTATGAGCTTTGA 59.992 43.478 13.81 0.00 39.69 2.69
6149 6238 1.194098 CTGCAACTTCTCGAAGCTGTG 59.806 52.381 10.65 6.59 41.99 3.66
6200 6289 2.579201 CTTGGCGTCGGGATCTGT 59.421 61.111 0.00 0.00 0.00 3.41
6201 6290 1.519455 CTTGGCGTCGGGATCTGTC 60.519 63.158 0.00 0.00 0.00 3.51
6369 6458 2.044946 AAGCTTGGCCCGATGTCC 60.045 61.111 0.00 0.00 0.00 4.02
6501 6596 6.002082 TCTCTAGGAATGAAATGCATCATGG 58.998 40.000 0.00 0.00 39.90 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.626654 CGTCAATCCGCTGTCCACAC 61.627 60.000 0.00 0.00 0.00 3.82
123 124 0.315251 TGTCTTCGTCCTGCAGACAG 59.685 55.000 17.39 5.58 46.69 3.51
181 182 0.178953 AAACAGCCCATCCAAGTGCT 60.179 50.000 0.00 0.00 33.52 4.40
261 262 0.178068 AGCCCGATCGTTGTAGCATT 59.822 50.000 15.09 0.00 0.00 3.56
298 299 0.333312 ACCAGGGTGTCAAAACCACA 59.667 50.000 0.00 0.00 42.47 4.17
323 324 1.961277 CAGAGCGACCAAGCCGTTT 60.961 57.895 0.00 0.00 38.01 3.60
324 325 2.357517 CAGAGCGACCAAGCCGTT 60.358 61.111 0.00 0.00 38.01 4.44
391 392 1.270826 CTTCTTCACGAGCTCCTGTGA 59.729 52.381 17.39 17.39 42.98 3.58
462 463 5.597813 AATCTCTCACAAAGCGTTGTAAG 57.402 39.130 17.71 13.35 46.47 2.34
493 494 3.263425 CCACCACCACTCCTACAAAGTAT 59.737 47.826 0.00 0.00 0.00 2.12
540 542 8.974060 AGACAATTTACAAGAGGTCTAACAAA 57.026 30.769 0.00 0.00 34.13 2.83
544 546 7.224297 AGCAAGACAATTTACAAGAGGTCTAA 58.776 34.615 0.00 0.00 34.75 2.10
619 622 3.486108 CGTAGCTGTGTCGGATACATTTC 59.514 47.826 8.06 1.76 41.10 2.17
630 633 1.870016 GCTCGCTCGTAGCTGTGTC 60.870 63.158 0.00 0.00 39.60 3.67
693 696 4.092116 AGAGTAGCCTTTTTGTCTGCTT 57.908 40.909 0.00 0.00 35.34 3.91
791 805 7.147976 CGGGATCTGTTTTTGAGAAGATTTTT 58.852 34.615 0.00 0.00 29.59 1.94
792 806 6.681777 CGGGATCTGTTTTTGAGAAGATTTT 58.318 36.000 0.00 0.00 29.59 1.82
793 807 5.335976 GCGGGATCTGTTTTTGAGAAGATTT 60.336 40.000 0.00 0.00 29.59 2.17
794 808 4.156739 GCGGGATCTGTTTTTGAGAAGATT 59.843 41.667 0.00 0.00 29.59 2.40
795 809 3.691609 GCGGGATCTGTTTTTGAGAAGAT 59.308 43.478 0.00 0.00 32.10 2.40
796 810 3.074412 GCGGGATCTGTTTTTGAGAAGA 58.926 45.455 0.00 0.00 0.00 2.87
797 811 3.077359 AGCGGGATCTGTTTTTGAGAAG 58.923 45.455 0.00 0.00 0.00 2.85
798 812 3.074412 GAGCGGGATCTGTTTTTGAGAA 58.926 45.455 0.00 0.00 0.00 2.87
799 813 2.615493 GGAGCGGGATCTGTTTTTGAGA 60.615 50.000 0.00 0.00 0.00 3.27
874 889 1.213296 ATGGCGGATCTTAGGGTTGT 58.787 50.000 0.00 0.00 0.00 3.32
1276 1292 3.879892 GAGAATCCACCTGGTATTTCTGC 59.120 47.826 17.65 9.34 33.54 4.26
1314 1332 0.771127 ACTAAACAGGAGGCAAGGCA 59.229 50.000 0.00 0.00 0.00 4.75
1409 1431 3.468140 GTCTCGGCCTACCCACCC 61.468 72.222 0.00 0.00 0.00 4.61
1469 1491 3.243704 GCGCAGATTAGAGAGTCCAGAAT 60.244 47.826 0.30 0.00 0.00 2.40
1496 1518 0.537828 GGGGCGGGACAAACTACAAA 60.538 55.000 0.00 0.00 0.00 2.83
1572 1596 1.168714 GCAGGACCAGAACCACATTC 58.831 55.000 0.00 0.00 37.62 2.67
1575 1599 1.768684 GAGGCAGGACCAGAACCACA 61.769 60.000 0.00 0.00 43.14 4.17
1576 1600 1.003233 GAGGCAGGACCAGAACCAC 60.003 63.158 0.00 0.00 43.14 4.16
1577 1601 0.116342 TAGAGGCAGGACCAGAACCA 59.884 55.000 0.00 0.00 43.14 3.67
1578 1602 1.066071 GTTAGAGGCAGGACCAGAACC 60.066 57.143 0.00 0.00 43.14 3.62
1615 1641 8.417106 TCAGTTCAGAATAGCAGGAAATAGTAG 58.583 37.037 0.00 0.00 0.00 2.57
1806 1832 1.575244 TGTCTGCAGCATCGATTAGC 58.425 50.000 9.47 0.00 0.00 3.09
1883 1909 5.178252 CCAATTCAGTCAGTACAGTCAACAG 59.822 44.000 0.00 0.00 0.00 3.16
2058 2084 5.479027 GCTCCTTGGTCCATAAAAGGTAAAA 59.521 40.000 7.14 0.00 41.12 1.52
2063 2089 3.085952 TGCTCCTTGGTCCATAAAAGG 57.914 47.619 1.26 1.26 41.60 3.11
2136 2162 1.943340 GCAATCCTAGCCTCCTTTTCG 59.057 52.381 0.00 0.00 0.00 3.46
2399 2425 3.114809 TGTTTCAGCATTCTTTGTTGCG 58.885 40.909 0.00 0.00 43.61 4.85
2510 2536 9.435688 GAAAACTGAAATATTACCTTTGCCATT 57.564 29.630 0.00 0.00 0.00 3.16
2546 2574 5.296813 AGTTTAAGGCGTAAAGAATGCAG 57.703 39.130 5.86 0.00 42.33 4.41
2665 2693 2.353605 CCTCTGAGAGCTTCAACCTCAC 60.354 54.545 6.17 0.00 34.81 3.51
2686 2714 6.093633 GTCATCCCTTACTTGGTGTAATTCAC 59.906 42.308 0.00 0.00 45.47 3.18
2927 2963 8.538856 TGAATTTGCAGTGTTTTAATTTTCTCG 58.461 29.630 0.00 0.00 0.00 4.04
3239 3276 7.819644 TCATTGTCTCCATAGTTGTCAAATTG 58.180 34.615 0.00 0.00 0.00 2.32
3881 3920 5.764686 AGATGAAGTGCACAGTGATTAACAA 59.235 36.000 21.04 0.00 0.00 2.83
4435 4475 4.271049 CGTTTGAGCAGAGAAGAAACTTCA 59.729 41.667 12.86 0.00 0.00 3.02
4700 4740 7.506114 TCTTTGGAGAGTTAGCTGAGTAAAAA 58.494 34.615 0.00 0.00 0.00 1.94
4701 4741 7.062749 TCTTTGGAGAGTTAGCTGAGTAAAA 57.937 36.000 0.00 0.00 0.00 1.52
4702 4742 6.665992 TCTTTGGAGAGTTAGCTGAGTAAA 57.334 37.500 0.00 0.00 0.00 2.01
4703 4743 6.274157 CTCTTTGGAGAGTTAGCTGAGTAA 57.726 41.667 0.00 0.00 43.66 2.24
4704 4744 5.906113 CTCTTTGGAGAGTTAGCTGAGTA 57.094 43.478 0.00 0.00 43.66 2.59
4705 4745 4.799564 CTCTTTGGAGAGTTAGCTGAGT 57.200 45.455 0.00 0.00 43.66 3.41
4850 4891 6.701841 TGAAAACACAGTGACTTCTAGATGAC 59.298 38.462 7.81 6.86 0.00 3.06
4880 4921 9.184523 CATACCTCATTTACACCAAAAATCCTA 57.815 33.333 0.00 0.00 0.00 2.94
4881 4922 7.673926 ACATACCTCATTTACACCAAAAATCCT 59.326 33.333 0.00 0.00 0.00 3.24
4921 4962 7.894376 AAAGGTTATGCATGAATTGAACTTG 57.106 32.000 10.16 0.00 0.00 3.16
5110 5151 7.696453 GTGCTATTGATGTTACAAATGTACACC 59.304 37.037 0.00 0.00 33.44 4.16
5331 5372 5.959618 ATACAAGGAAAACAGTTGTAGGC 57.040 39.130 0.00 0.00 39.40 3.93
5353 5394 0.608856 CACCCAAGCATGGCTGTGTA 60.609 55.000 1.35 0.00 46.09 2.90
5357 5398 2.036098 TCCACCCAAGCATGGCTG 59.964 61.111 1.35 0.00 46.09 4.85
5358 5399 2.233566 TCTCCACCCAAGCATGGCT 61.234 57.895 1.35 0.00 46.09 4.75
5380 5421 4.578928 AGGTTCACAAACATTAGCGTCTTT 59.421 37.500 0.00 0.00 37.10 2.52
5402 5443 0.037232 GAAGACACTTCCGGGGACAG 60.037 60.000 0.00 0.00 0.00 3.51
5443 5484 1.441016 CCGAGCAGCAAAACGAAGC 60.441 57.895 0.00 0.00 0.00 3.86
5530 5571 5.942236 ACTTGACAGTGAATTGACTGCATAT 59.058 36.000 22.89 5.35 46.28 1.78
5864 5905 2.297033 ACAAGCCAAGCCATAACAACAG 59.703 45.455 0.00 0.00 0.00 3.16
6022 6111 0.972883 GCCTAGCCAGTATCCAGGAG 59.027 60.000 0.00 0.00 0.00 3.69
6077 6166 2.100128 AGGATCCTGCTATGCTGACT 57.900 50.000 15.29 0.00 0.00 3.41
6149 6238 1.153349 CTAGCCAACCGCCTCTTCC 60.153 63.158 0.00 0.00 38.78 3.46
6195 6284 1.227089 GCTCATCACCGCGACAGAT 60.227 57.895 8.23 4.71 0.00 2.90
6200 6289 1.446099 GACAAGCTCATCACCGCGA 60.446 57.895 8.23 0.00 0.00 5.87
6201 6290 2.792290 CGACAAGCTCATCACCGCG 61.792 63.158 0.00 0.00 0.00 6.46
6501 6596 7.015682 CCCATACATACTATATCACCTCATCCC 59.984 44.444 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.