Multiple sequence alignment - TraesCS3A01G068500

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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 TraesCS3A01G068500 chr3A 100.000 4086 0 0 1 4086 41047111 41051196 0.000000e+00 7546.0
1 TraesCS3A01G068500 chr3A 88.539 3272 340 22 823 4078 41149788 41153040 0.000000e+00 3932.0
2 TraesCS3A01G068500 chr3A 89.122 2620 273 8 1001 3614 41616718 41619331 0.000000e+00 3249.0
3 TraesCS3A01G068500 chr3A 83.541 3214 494 29 863 4058 40936241 40939437 0.000000e+00 2972.0
4 TraesCS3A01G068500 chr3A 93.361 1657 81 19 739 2370 40947026 40948678 0.000000e+00 2423.0
5 TraesCS3A01G068500 chr3A 86.515 749 95 4 3332 4079 41362908 41363651 0.000000e+00 819.0
6 TraesCS3A01G068500 chr3A 85.629 334 36 4 3 329 41177313 41177641 1.410000e-89 340.0
7 TraesCS3A01G068500 chr3A 81.418 409 56 11 326 717 41177672 41178077 2.370000e-82 316.0
8 TraesCS3A01G068500 chr3A 83.383 337 43 6 1 329 40946266 40946597 2.390000e-77 300.0
9 TraesCS3A01G068500 chr3B 89.155 3089 309 7 1001 4082 51802641 51805710 0.000000e+00 3825.0
10 TraesCS3A01G068500 chr3B 86.732 3354 409 26 739 4082 51243087 51246414 0.000000e+00 3696.0
11 TraesCS3A01G068500 chr3B 87.467 3048 365 11 1001 4041 52426330 52429367 0.000000e+00 3496.0
12 TraesCS3A01G068500 chr3B 87.159 3076 375 13 1020 4082 51249115 51252183 0.000000e+00 3474.0
13 TraesCS3A01G068500 chr3B 88.534 2756 295 16 1322 4070 52551643 52554384 0.000000e+00 3319.0
14 TraesCS3A01G068500 chr3B 83.882 3096 450 28 739 3805 51777099 51780174 0.000000e+00 2907.0
15 TraesCS3A01G068500 chr3B 93.061 807 54 1 3282 4086 52456916 52457722 0.000000e+00 1179.0
16 TraesCS3A01G068500 chr3B 85.683 461 50 4 3634 4086 51797009 51797461 4.780000e-129 472.0
17 TraesCS3A01G068500 chr3B 84.793 217 30 2 214 430 51924143 51924356 8.900000e-52 215.0
18 TraesCS3A01G068500 chr3B 77.835 388 49 25 326 705 51957959 51958317 5.350000e-49 206.0
19 TraesCS3A01G068500 chr3B 86.957 115 7 6 600 714 51242991 51243097 5.550000e-24 122.0
20 TraesCS3A01G068500 chr3B 74.307 397 47 35 326 714 51776760 51777109 2.580000e-22 117.0
21 TraesCS3A01G068500 chr3D 88.469 3096 340 11 1001 4082 30006701 30009793 0.000000e+00 3723.0
22 TraesCS3A01G068500 chr4D 100.000 29 0 0 716 744 69406090 69406062 2.000000e-03 54.7


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 TraesCS3A01G068500 chr3A 41047111 41051196 4085 False 7546.000000 7546 100.000000 1 4086 1 chr3A.!!$F2 4085
1 TraesCS3A01G068500 chr3A 41149788 41153040 3252 False 3932.000000 3932 88.539000 823 4078 1 chr3A.!!$F3 3255
2 TraesCS3A01G068500 chr3A 41616718 41619331 2613 False 3249.000000 3249 89.122000 1001 3614 1 chr3A.!!$F5 2613
3 TraesCS3A01G068500 chr3A 40936241 40939437 3196 False 2972.000000 2972 83.541000 863 4058 1 chr3A.!!$F1 3195
4 TraesCS3A01G068500 chr3A 40946266 40948678 2412 False 1361.500000 2423 88.372000 1 2370 2 chr3A.!!$F6 2369
5 TraesCS3A01G068500 chr3A 41362908 41363651 743 False 819.000000 819 86.515000 3332 4079 1 chr3A.!!$F4 747
6 TraesCS3A01G068500 chr3A 41177313 41178077 764 False 328.000000 340 83.523500 3 717 2 chr3A.!!$F7 714
7 TraesCS3A01G068500 chr3B 51802641 51805710 3069 False 3825.000000 3825 89.155000 1001 4082 1 chr3B.!!$F2 3081
8 TraesCS3A01G068500 chr3B 52426330 52429367 3037 False 3496.000000 3496 87.467000 1001 4041 1 chr3B.!!$F5 3040
9 TraesCS3A01G068500 chr3B 52551643 52554384 2741 False 3319.000000 3319 88.534000 1322 4070 1 chr3B.!!$F7 2748
10 TraesCS3A01G068500 chr3B 51242991 51252183 9192 False 2430.666667 3696 86.949333 600 4082 3 chr3B.!!$F8 3482
11 TraesCS3A01G068500 chr3B 51776760 51780174 3414 False 1512.000000 2907 79.094500 326 3805 2 chr3B.!!$F9 3479
12 TraesCS3A01G068500 chr3B 52456916 52457722 806 False 1179.000000 1179 93.061000 3282 4086 1 chr3B.!!$F6 804
13 TraesCS3A01G068500 chr3D 30006701 30009793 3092 False 3723.000000 3723 88.469000 1001 4082 1 chr3D.!!$F1 3081

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
737 802 0.105964 GGGCAAAAGCCTTTTTCGGT 59.894 50.0 0.00 0.0 34.34 4.69 F
796 861 0.631212 CTTGGCCTTACTCCCCCATT 59.369 55.0 3.32 0.0 0.00 3.16 F
1806 1904 0.949397 TGCAGAGAAAGCTTGCACAG 59.051 50.0 7.33 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 1763 0.449388 CGTGCATCTTGAAGCTTCCC 59.551 55.000 23.42 0.62 0.00 3.97 R
2343 2448 0.873743 GCTCCTCGATGAAGCCTTCG 60.874 60.000 0.00 0.00 40.15 3.79 R
3742 9621 1.072965 ACTGAGTTCCTTCAAGCAGGG 59.927 52.381 0.00 0.00 34.24 4.45 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
39 40 1.499049 AGTTTCGTCTCGGTTGCTTC 58.501 50.000 0.00 0.00 0.00 3.86
49 50 0.438830 CGGTTGCTTCTGTTAGTCGC 59.561 55.000 0.00 0.00 0.00 5.19
50 51 0.438830 GGTTGCTTCTGTTAGTCGCG 59.561 55.000 0.00 0.00 0.00 5.87
51 52 0.179248 GTTGCTTCTGTTAGTCGCGC 60.179 55.000 0.00 0.00 0.00 6.86
73 74 1.224069 CTGTTGCTCCACAGGTCACG 61.224 60.000 3.97 0.00 40.60 4.35
93 94 3.055819 ACGTATGCTTGAACTGATCCTGT 60.056 43.478 0.00 0.00 0.00 4.00
148 149 4.218635 CAGTGGCTTCTCAGTCTAGTTACA 59.781 45.833 0.00 0.00 0.00 2.41
157 158 5.590663 TCTCAGTCTAGTTACAGGCATGTAG 59.409 44.000 11.49 1.85 42.72 2.74
158 159 5.262009 TCAGTCTAGTTACAGGCATGTAGT 58.738 41.667 11.49 6.06 42.72 2.73
159 160 6.420638 TCAGTCTAGTTACAGGCATGTAGTA 58.579 40.000 11.49 6.87 42.72 1.82
169 170 5.858381 ACAGGCATGTAGTATTCAGGTATG 58.142 41.667 0.06 0.00 38.09 2.39
173 174 5.352569 GGCATGTAGTATTCAGGTATGCATC 59.647 44.000 0.19 0.00 40.71 3.91
202 203 0.388520 TGTTCTGCACGTCTGGATCG 60.389 55.000 0.00 0.00 0.00 3.69
234 242 7.278424 ACAATCTTTTGTTCACTTGTTGATTGG 59.722 33.333 13.82 0.78 43.57 3.16
310 318 9.781834 GATTGACCGATACTCTTCTATTATCTG 57.218 37.037 0.00 0.00 0.00 2.90
329 372 4.394729 TCTGTTTTTATTCTCGCTTGGGT 58.605 39.130 0.00 0.00 0.00 4.51
332 375 4.339814 TGTTTTTATTCTCGCTTGGGTTGT 59.660 37.500 0.00 0.00 0.00 3.32
414 457 1.072331 TCCTTGCTGGAAGACTGGTTC 59.928 52.381 10.73 0.00 42.94 3.62
430 473 4.243270 CTGGTTCGTAAGGTAAGACTTGG 58.757 47.826 0.00 0.00 38.47 3.61
431 474 2.998670 GGTTCGTAAGGTAAGACTTGGC 59.001 50.000 0.00 0.00 38.47 4.52
435 478 3.512329 TCGTAAGGTAAGACTTGGCATCA 59.488 43.478 0.00 0.00 38.47 3.07
441 484 6.808321 AGGTAAGACTTGGCATCATACTTA 57.192 37.500 0.00 0.00 0.00 2.24
449 492 5.819901 ACTTGGCATCATACTTAAGAGCTTC 59.180 40.000 10.09 0.00 0.00 3.86
470 513 7.389053 AGCTTCCAACTTTACTTTCATGACTAG 59.611 37.037 0.00 0.00 0.00 2.57
471 514 7.173390 GCTTCCAACTTTACTTTCATGACTAGT 59.827 37.037 12.80 12.80 0.00 2.57
472 515 9.706691 CTTCCAACTTTACTTTCATGACTAGTA 57.293 33.333 11.16 11.16 0.00 1.82
473 516 9.485206 TTCCAACTTTACTTTCATGACTAGTAC 57.515 33.333 13.74 0.00 0.00 2.73
476 519 8.425491 CAACTTTACTTTCATGACTAGTACGTG 58.575 37.037 13.74 1.90 0.00 4.49
477 520 7.655490 ACTTTACTTTCATGACTAGTACGTGT 58.345 34.615 13.74 10.74 0.00 4.49
478 521 8.786898 ACTTTACTTTCATGACTAGTACGTGTA 58.213 33.333 13.74 0.00 0.00 2.90
479 522 8.955061 TTTACTTTCATGACTAGTACGTGTAC 57.045 34.615 13.74 1.90 36.35 2.90
497 542 7.327975 ACGTGTACTTATCATGATTTCTGGAA 58.672 34.615 14.65 0.00 0.00 3.53
498 543 7.822334 ACGTGTACTTATCATGATTTCTGGAAA 59.178 33.333 14.65 0.00 34.46 3.13
499 544 8.830580 CGTGTACTTATCATGATTTCTGGAAAT 58.169 33.333 14.65 8.11 43.14 2.17
533 591 9.813080 GTGTTAAGATAGATCTGACAAACAAAC 57.187 33.333 5.18 0.97 36.32 2.93
565 625 8.738645 AACAGGATGATTAATCTGTAGGTTTC 57.261 34.615 16.24 1.79 39.69 2.78
575 635 4.336889 TCTGTAGGTTTCAACTCAGTGG 57.663 45.455 0.00 0.00 0.00 4.00
582 642 4.956075 AGGTTTCAACTCAGTGGAACATTT 59.044 37.500 0.00 0.00 44.52 2.32
584 644 6.777580 AGGTTTCAACTCAGTGGAACATTTAT 59.222 34.615 0.00 0.00 44.52 1.40
588 648 8.684386 TTCAACTCAGTGGAACATTTATTGTA 57.316 30.769 0.00 0.00 44.52 2.41
631 691 5.366460 CATCTGATGGCTATTCAACTGAGT 58.634 41.667 9.82 0.00 0.00 3.41
640 700 7.422399 TGGCTATTCAACTGAGTAAAACAAAC 58.578 34.615 0.00 0.00 0.00 2.93
714 779 8.707938 GCACAAAGCAAATAAAAGGATAGAAT 57.292 30.769 0.00 0.00 44.79 2.40
715 780 8.598075 GCACAAAGCAAATAAAAGGATAGAATG 58.402 33.333 0.00 0.00 44.79 2.67
716 781 8.598075 CACAAAGCAAATAAAAGGATAGAATGC 58.402 33.333 0.00 0.00 0.00 3.56
717 782 7.489113 ACAAAGCAAATAAAAGGATAGAATGCG 59.511 33.333 0.00 0.00 36.45 4.73
718 783 6.076981 AGCAAATAAAAGGATAGAATGCGG 57.923 37.500 0.00 0.00 36.45 5.69
719 784 5.010012 AGCAAATAAAAGGATAGAATGCGGG 59.990 40.000 0.00 0.00 36.45 6.13
720 785 5.772521 CAAATAAAAGGATAGAATGCGGGG 58.227 41.667 0.00 0.00 0.00 5.73
721 786 1.692411 AAAAGGATAGAATGCGGGGC 58.308 50.000 0.00 0.00 0.00 5.80
722 787 0.550914 AAAGGATAGAATGCGGGGCA 59.449 50.000 0.00 0.00 44.86 5.36
723 788 0.550914 AAGGATAGAATGCGGGGCAA 59.449 50.000 0.00 0.00 43.62 4.52
724 789 0.550914 AGGATAGAATGCGGGGCAAA 59.449 50.000 0.00 0.00 43.62 3.68
725 790 1.064017 AGGATAGAATGCGGGGCAAAA 60.064 47.619 0.00 0.00 43.62 2.44
726 791 1.338020 GGATAGAATGCGGGGCAAAAG 59.662 52.381 0.00 0.00 43.62 2.27
727 792 0.746659 ATAGAATGCGGGGCAAAAGC 59.253 50.000 0.00 0.00 43.62 3.51
728 793 1.319614 TAGAATGCGGGGCAAAAGCC 61.320 55.000 0.00 0.00 43.62 4.35
729 794 2.604382 AATGCGGGGCAAAAGCCT 60.604 55.556 6.45 0.00 43.62 4.58
730 795 2.171209 GAATGCGGGGCAAAAGCCTT 62.171 55.000 6.45 0.00 43.62 4.35
731 796 1.767654 AATGCGGGGCAAAAGCCTTT 61.768 50.000 6.45 0.00 43.62 3.11
732 797 1.767654 ATGCGGGGCAAAAGCCTTTT 61.768 50.000 6.45 0.00 43.62 2.27
733 798 1.227823 GCGGGGCAAAAGCCTTTTT 60.228 52.632 0.00 0.00 36.97 1.94
734 799 1.227999 GCGGGGCAAAAGCCTTTTTC 61.228 55.000 0.00 0.00 34.34 2.29
735 800 0.943835 CGGGGCAAAAGCCTTTTTCG 60.944 55.000 0.00 0.00 34.34 3.46
736 801 0.602638 GGGGCAAAAGCCTTTTTCGG 60.603 55.000 0.00 0.00 34.34 4.30
737 802 0.105964 GGGCAAAAGCCTTTTTCGGT 59.894 50.000 0.00 0.00 34.34 4.69
738 803 1.341852 GGGCAAAAGCCTTTTTCGGTA 59.658 47.619 0.00 0.00 34.34 4.02
787 852 4.489306 AGACCTCAATACTTGGCCTTAC 57.511 45.455 3.32 0.00 0.00 2.34
791 856 3.433740 CCTCAATACTTGGCCTTACTCCC 60.434 52.174 3.32 0.00 0.00 4.30
793 858 1.519498 ATACTTGGCCTTACTCCCCC 58.481 55.000 3.32 0.00 0.00 5.40
796 861 0.631212 CTTGGCCTTACTCCCCCATT 59.369 55.000 3.32 0.00 0.00 3.16
827 892 9.791801 TGTTGCATAGCTCCATTATTCTAAATA 57.208 29.630 0.00 0.00 0.00 1.40
852 917 8.813643 ACGTTAAATATCTTCTATGCCAGTAC 57.186 34.615 0.00 0.00 0.00 2.73
915 1006 7.888021 ACATACCTTGTGTATTCATTTTCAGGA 59.112 33.333 0.00 0.00 38.10 3.86
946 1038 5.682943 TTACCATTCTCCAAAACAAGTCG 57.317 39.130 0.00 0.00 0.00 4.18
1351 1449 3.539604 TCTTGTTTTTGCAACATTGGGG 58.460 40.909 0.00 0.00 0.00 4.96
1382 1480 5.000591 TGATGTTGCTGTTCGGATTAGAAA 58.999 37.500 0.00 0.00 0.00 2.52
1509 1607 1.118838 CCAACCTTGTTGAGCCCAAA 58.881 50.000 8.47 0.00 33.49 3.28
1530 1628 4.510167 ACTTGTGGGGAAGGAGATTATG 57.490 45.455 0.00 0.00 0.00 1.90
1538 1636 5.372363 TGGGGAAGGAGATTATGCATTCTAA 59.628 40.000 3.54 0.00 0.00 2.10
1806 1904 0.949397 TGCAGAGAAAGCTTGCACAG 59.051 50.000 7.33 0.00 0.00 3.66
1947 2051 8.788806 ACCACACGAGATTATCAAATTACAAAA 58.211 29.630 0.00 0.00 0.00 2.44
2037 2141 3.626670 GGAAGAGCATGAACATTGAGGAG 59.373 47.826 0.00 0.00 0.00 3.69
2129 2234 3.596214 CAATCAAGGTTACCGCTAGTGT 58.404 45.455 1.99 0.00 0.00 3.55
2343 2448 3.898482 AGTTACCTGGTTATGGATTGCC 58.102 45.455 3.84 0.00 0.00 4.52
2591 8452 5.684184 TGCGACGTATTACTGCTGTTATTAG 59.316 40.000 0.09 0.00 0.00 1.73
2615 8476 6.053650 GGAAGGATATGTTGGTGTTACCTAC 58.946 44.000 5.77 5.77 42.97 3.18
3024 8885 7.683578 CAGATTATCCTATTGGTGATGGAAGA 58.316 38.462 0.00 0.00 31.87 2.87
3121 8982 7.781056 TCTTGTTAAATTGGAAAGAGCAACTT 58.219 30.769 0.00 0.00 40.98 2.66
3274 9138 1.192146 TCCGCACAACCTAGAAGGCT 61.192 55.000 0.00 0.00 39.63 4.58
3339 9203 2.158726 TGGTACCACCTGTTTGTCTTCC 60.159 50.000 11.60 0.00 39.58 3.46
3343 9207 4.724279 ACCACCTGTTTGTCTTCCTTAT 57.276 40.909 0.00 0.00 0.00 1.73
3670 9549 4.082523 GGGTGCGACTGCTGCCTA 62.083 66.667 0.00 0.00 43.34 3.93
3742 9621 0.178990 ACAGCTTGGAAAGGACACCC 60.179 55.000 0.00 0.00 46.35 4.61
3756 9635 1.360393 ACACCCCCTGCTTGAAGGAA 61.360 55.000 0.00 0.00 40.02 3.36
3936 9815 2.431683 GGGCTGGACAGTCTGCAA 59.568 61.111 16.81 0.00 32.63 4.08
3970 9849 2.362397 GACGAGGATATGCAAGAGGTCA 59.638 50.000 0.00 0.00 0.00 4.02
4000 9879 1.676967 GTGCCTGGGCTTCAAGAGG 60.677 63.158 13.05 0.00 42.51 3.69
4042 9921 4.760715 GCGAAGACCTGGATATCTACACTA 59.239 45.833 0.00 0.00 0.00 2.74
4058 9950 7.441890 TCTACACTATCTAGCAGTTAGATGC 57.558 40.000 15.30 0.00 46.30 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 0.388649 AACAGGAGCGCGACTAACAG 60.389 55.000 12.10 3.20 0.00 3.16
49 50 2.031012 TGTGGAGCAACAGGAGCG 59.969 61.111 0.00 0.00 37.01 5.03
50 51 3.978272 CTGTGGAGCAACAGGAGC 58.022 61.111 6.37 0.00 43.22 4.70
69 70 3.195610 AGGATCAGTTCAAGCATACGTGA 59.804 43.478 0.00 0.00 32.09 4.35
73 74 3.064545 GCACAGGATCAGTTCAAGCATAC 59.935 47.826 0.00 0.00 0.00 2.39
93 94 2.124109 AGATCGAGGAGAGCGGCA 60.124 61.111 1.45 0.00 40.85 5.69
134 135 4.727507 ACATGCCTGTAACTAGACTGAG 57.272 45.455 0.00 0.00 32.49 3.35
148 149 4.347876 TGCATACCTGAATACTACATGCCT 59.652 41.667 0.00 0.00 37.17 4.75
157 158 2.996621 GAGCCGATGCATACCTGAATAC 59.003 50.000 0.00 0.00 41.13 1.89
158 159 2.899900 AGAGCCGATGCATACCTGAATA 59.100 45.455 0.00 0.00 41.13 1.75
159 160 1.696336 AGAGCCGATGCATACCTGAAT 59.304 47.619 0.00 0.00 41.13 2.57
169 170 0.108424 AGAACACTGAGAGCCGATGC 60.108 55.000 0.00 0.00 37.95 3.91
173 174 1.005748 TGCAGAACACTGAGAGCCG 60.006 57.895 0.00 0.00 33.94 5.52
193 194 3.786635 AGATTGTGTTAGCGATCCAGAC 58.213 45.455 0.00 0.00 31.24 3.51
234 242 8.276325 CACCTGCGATACAAAATAGAAGATTAC 58.724 37.037 0.00 0.00 0.00 1.89
253 261 2.466982 CCATGCTGCTACACCTGCG 61.467 63.158 0.00 0.00 33.01 5.18
310 318 4.866921 ACAACCCAAGCGAGAATAAAAAC 58.133 39.130 0.00 0.00 0.00 2.43
329 372 2.037902 TGCAGTTTACTCCGATGGACAA 59.962 45.455 0.00 0.00 0.00 3.18
332 375 2.766263 AGATGCAGTTTACTCCGATGGA 59.234 45.455 0.00 0.00 0.00 3.41
414 457 3.857052 TGATGCCAAGTCTTACCTTACG 58.143 45.455 0.00 0.00 0.00 3.18
430 473 5.819901 AGTTGGAAGCTCTTAAGTATGATGC 59.180 40.000 1.63 0.00 0.00 3.91
431 474 7.856145 AAGTTGGAAGCTCTTAAGTATGATG 57.144 36.000 1.63 0.00 0.00 3.07
435 478 9.794719 AAAGTAAAGTTGGAAGCTCTTAAGTAT 57.205 29.630 1.63 0.00 0.00 2.12
441 484 6.772716 TCATGAAAGTAAAGTTGGAAGCTCTT 59.227 34.615 0.00 0.00 0.00 2.85
449 492 7.597743 ACGTACTAGTCATGAAAGTAAAGTTGG 59.402 37.037 16.76 8.12 0.00 3.77
470 513 7.919091 TCCAGAAATCATGATAAGTACACGTAC 59.081 37.037 9.04 0.00 36.35 3.67
471 514 8.002984 TCCAGAAATCATGATAAGTACACGTA 57.997 34.615 9.04 0.00 0.00 3.57
472 515 6.873997 TCCAGAAATCATGATAAGTACACGT 58.126 36.000 9.04 0.00 0.00 4.49
473 516 7.770801 TTCCAGAAATCATGATAAGTACACG 57.229 36.000 9.04 0.00 0.00 4.49
508 566 9.554395 TGTTTGTTTGTCAGATCTATCTTAACA 57.446 29.630 0.00 0.45 34.22 2.41
541 599 7.861629 TGAAACCTACAGATTAATCATCCTGT 58.138 34.615 17.56 14.13 31.20 4.00
543 601 8.552296 AGTTGAAACCTACAGATTAATCATCCT 58.448 33.333 17.56 0.00 31.20 3.24
560 620 4.918810 AATGTTCCACTGAGTTGAAACC 57.081 40.909 0.26 0.00 0.00 3.27
575 635 7.965107 GCATAGCAGCCTATACAATAAATGTTC 59.035 37.037 0.00 0.00 43.63 3.18
699 764 3.826729 GCCCCGCATTCTATCCTTTTATT 59.173 43.478 0.00 0.00 0.00 1.40
704 769 0.550914 TTGCCCCGCATTCTATCCTT 59.449 50.000 0.00 0.00 38.76 3.36
705 770 0.550914 TTTGCCCCGCATTCTATCCT 59.449 50.000 0.00 0.00 38.76 3.24
706 771 1.338020 CTTTTGCCCCGCATTCTATCC 59.662 52.381 0.00 0.00 38.76 2.59
707 772 1.269257 GCTTTTGCCCCGCATTCTATC 60.269 52.381 0.00 0.00 38.76 2.08
708 773 0.746659 GCTTTTGCCCCGCATTCTAT 59.253 50.000 0.00 0.00 38.76 1.98
709 774 2.188912 GCTTTTGCCCCGCATTCTA 58.811 52.632 0.00 0.00 38.76 2.10
710 775 2.973082 GCTTTTGCCCCGCATTCT 59.027 55.556 0.00 0.00 38.76 2.40
720 785 3.493129 CCTTTACCGAAAAAGGCTTTTGC 59.507 43.478 24.73 21.78 46.66 3.68
728 793 5.154222 GCATTCTGTCCTTTACCGAAAAAG 58.846 41.667 3.29 3.29 35.32 2.27
729 794 4.022676 GGCATTCTGTCCTTTACCGAAAAA 60.023 41.667 0.00 0.00 35.32 1.94
730 795 3.504520 GGCATTCTGTCCTTTACCGAAAA 59.495 43.478 0.00 0.00 35.32 2.29
731 796 3.078837 GGCATTCTGTCCTTTACCGAAA 58.921 45.455 0.00 0.00 35.32 3.46
732 797 2.039216 TGGCATTCTGTCCTTTACCGAA 59.961 45.455 0.00 0.00 36.01 4.30
733 798 1.626321 TGGCATTCTGTCCTTTACCGA 59.374 47.619 0.00 0.00 0.00 4.69
734 799 2.107950 TGGCATTCTGTCCTTTACCG 57.892 50.000 0.00 0.00 0.00 4.02
735 800 3.421844 AGTTGGCATTCTGTCCTTTACC 58.578 45.455 0.00 0.00 0.00 2.85
736 801 4.072131 TGAGTTGGCATTCTGTCCTTTAC 58.928 43.478 0.00 0.00 0.00 2.01
737 802 4.326826 CTGAGTTGGCATTCTGTCCTTTA 58.673 43.478 0.00 0.00 0.00 1.85
738 803 3.152341 CTGAGTTGGCATTCTGTCCTTT 58.848 45.455 0.00 0.00 0.00 3.11
787 852 2.455557 TGCAACATACAAATGGGGGAG 58.544 47.619 0.00 0.00 37.43 4.30
791 856 4.261741 GGAGCTATGCAACATACAAATGGG 60.262 45.833 0.00 0.00 37.43 4.00
793 858 5.503662 TGGAGCTATGCAACATACAAATG 57.496 39.130 0.00 0.00 39.17 2.32
796 861 7.720957 AGAATAATGGAGCTATGCAACATACAA 59.279 33.333 0.00 0.00 29.79 2.41
827 892 8.418662 TGTACTGGCATAGAAGATATTTAACGT 58.581 33.333 0.00 0.00 0.00 3.99
852 917 9.676195 CACAGTGACATAAGTCTCTCTAATATG 57.324 37.037 0.00 0.00 44.38 1.78
874 962 7.326789 CACAAGGTATGTTAATTGCTTTCACAG 59.673 37.037 0.00 0.00 41.46 3.66
915 1006 7.070571 TGTTTTGGAGAATGGTAAAAGGTGAAT 59.929 33.333 0.00 0.00 0.00 2.57
926 1018 2.293399 GCGACTTGTTTTGGAGAATGGT 59.707 45.455 0.00 0.00 0.00 3.55
1351 1449 3.726517 AGCAACATCACGGCGTGC 61.727 61.111 33.59 21.40 32.98 5.34
1509 1607 3.372025 GCATAATCTCCTTCCCCACAAGT 60.372 47.826 0.00 0.00 0.00 3.16
1530 1628 3.191371 CCACCAACTTCCTGTTAGAATGC 59.809 47.826 0.00 0.00 37.07 3.56
1538 1636 3.046374 ACTAAGTCCACCAACTTCCTGT 58.954 45.455 0.00 0.00 40.01 4.00
1661 1759 3.006217 GTGCATCTTGAAGCTTCCCTTTT 59.994 43.478 23.42 2.31 32.78 2.27
1665 1763 0.449388 CGTGCATCTTGAAGCTTCCC 59.551 55.000 23.42 0.62 0.00 3.97
1806 1904 8.138074 AGAAAGAAACTCTTGCCTTTAATTGTC 58.862 33.333 0.00 0.00 36.71 3.18
1947 2051 5.535029 TGGGTATGGTCTACACCTATTCTT 58.465 41.667 0.00 0.00 44.17 2.52
2037 2141 6.981722 TCTTAAATTCTGCACTTCCTTTTCC 58.018 36.000 0.00 0.00 0.00 3.13
2129 2234 6.112734 TCTGTTAGTTCTCTGCTTGACAAAA 58.887 36.000 0.00 0.00 0.00 2.44
2343 2448 0.873743 GCTCCTCGATGAAGCCTTCG 60.874 60.000 0.00 0.00 40.15 3.79
2591 8452 5.112129 AGGTAACACCAACATATCCTTCC 57.888 43.478 0.00 0.00 41.95 3.46
2615 8476 5.186198 CCTTAACTTCCACCTTATCCACTG 58.814 45.833 0.00 0.00 0.00 3.66
2999 8860 7.683578 TCTTCCATCACCAATAGGATAATCTG 58.316 38.462 0.00 0.00 38.69 2.90
3024 8885 5.958380 TCCATCTTGTACAACAGTATCCTCT 59.042 40.000 3.59 0.00 0.00 3.69
3121 8982 5.147330 AGCACTGTATTTGTACTGCAGTA 57.853 39.130 22.67 22.67 38.21 2.74
3174 9035 1.202582 CCACGTTCAGTCCACTCTAGG 59.797 57.143 0.00 0.00 0.00 3.02
3670 9549 4.869861 GTGAAGTTGCAATTCCAACAAACT 59.130 37.500 14.52 0.00 45.73 2.66
3742 9621 1.072965 ACTGAGTTCCTTCAAGCAGGG 59.927 52.381 0.00 0.00 34.24 4.45
3756 9635 7.793036 AGTTGTTTAGTCCTCTTAAACTGAGT 58.207 34.615 8.72 0.00 35.42 3.41
4000 9879 2.125512 ATGAAGTCGCCGGTGCTC 60.126 61.111 11.05 7.36 34.43 4.26
4042 9921 4.040217 CCTTGAGGCATCTAACTGCTAGAT 59.960 45.833 0.00 0.00 46.55 1.98
4058 9950 5.934625 GGCAGTGTTCATATATACCTTGAGG 59.065 44.000 0.00 0.00 42.17 3.86


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

AutoCloner maintained by Alex Coulton.