Multiple sequence alignment - TraesCS5D01G084800

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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 TraesCS5D01G084800 chr5D 100.000 5366 0 0 1 5366 88880265 88874900 0.000000e+00 9910.0
1 TraesCS5D01G084800 chr5D 87.379 103 13 0 1548 1650 6108593 6108491 9.440000e-23 119.0
2 TraesCS5D01G084800 chr5A 95.244 4479 129 26 701 5127 82872455 82868009 0.000000e+00 7014.0
3 TraesCS5D01G084800 chr5A 92.537 67 3 1 5165 5231 82868018 82867954 1.590000e-15 95.3
4 TraesCS5D01G084800 chr5B 96.270 3190 60 10 1807 4971 95513170 95516325 0.000000e+00 5177.0
5 TraesCS5D01G084800 chr5B 96.506 1202 32 2 698 1889 95511977 95513178 0.000000e+00 1978.0
6 TraesCS5D01G084800 chr5B 88.356 584 43 12 2537 3107 53664967 53665538 0.000000e+00 678.0
7 TraesCS5D01G084800 chr5B 91.268 355 22 7 5001 5350 95516326 95516676 4.860000e-130 475.0
8 TraesCS5D01G084800 chr5B 88.350 103 12 0 1548 1650 690647367 690647265 2.030000e-24 124.0
9 TraesCS5D01G084800 chr7D 86.339 549 71 4 3 549 478799469 478798923 3.580000e-166 595.0
10 TraesCS5D01G084800 chr7D 81.304 690 98 22 24 698 636717084 636717757 1.020000e-146 531.0
11 TraesCS5D01G084800 chr7D 87.805 123 12 2 5224 5346 596440156 596440037 2.010000e-29 141.0
12 TraesCS5D01G084800 chr7D 87.603 121 13 2 5226 5345 351907074 351906955 7.250000e-29 139.0
13 TraesCS5D01G084800 chr3B 86.472 547 69 5 3 546 708392116 708392660 3.580000e-166 595.0
14 TraesCS5D01G084800 chr3B 93.333 135 7 2 3177 3311 117589430 117589298 1.180000e-46 198.0
15 TraesCS5D01G084800 chr3B 91.912 136 11 0 3177 3312 42630984 42630849 1.970000e-44 191.0
16 TraesCS5D01G084800 chr3B 88.136 118 12 2 5229 5345 10717871 10717987 7.250000e-29 139.0
17 TraesCS5D01G084800 chr7B 86.182 550 71 5 3 549 739379942 739379395 1.660000e-164 590.0
18 TraesCS5D01G084800 chr7B 80.392 714 118 19 3 698 707963846 707963137 1.710000e-144 523.0
19 TraesCS5D01G084800 chr7B 91.971 137 11 0 3176 3312 522721480 522721344 5.480000e-45 193.0
20 TraesCS5D01G084800 chr4A 87.170 530 48 9 2590 3110 58720871 58720353 7.740000e-163 584.0
21 TraesCS5D01G084800 chr4A 87.603 121 11 4 5227 5345 594278520 594278638 2.610000e-28 137.0
22 TraesCS5D01G084800 chr4A 94.118 51 2 1 2537 2586 58786705 58786655 5.760000e-10 76.8
23 TraesCS5D01G084800 chr1B 85.818 550 73 5 3 549 94009779 94009232 3.600000e-161 579.0
24 TraesCS5D01G084800 chr6B 80.699 715 114 21 3 699 706517237 706516529 7.910000e-148 534.0
25 TraesCS5D01G084800 chr3D 81.124 694 96 26 24 698 489527699 489528376 1.710000e-144 523.0
26 TraesCS5D01G084800 chr3D 80.456 701 119 18 3 691 614469664 614468970 2.220000e-143 520.0
27 TraesCS5D01G084800 chr3D 89.732 224 23 0 1548 1771 382002131 382002354 2.450000e-73 287.0
28 TraesCS5D01G084800 chr3D 91.912 136 11 0 3177 3312 71517844 71517709 1.970000e-44 191.0
29 TraesCS5D01G084800 chr3D 87.903 124 13 2 5224 5346 557470733 557470855 1.560000e-30 145.0
30 TraesCS5D01G084800 chr2B 87.901 405 29 5 2540 2925 10728516 10728919 4.900000e-125 459.0
31 TraesCS5D01G084800 chr2B 86.096 187 17 4 2921 3107 10741579 10741756 5.480000e-45 193.0
32 TraesCS5D01G084800 chr2B 92.373 118 8 1 1654 1771 574708122 574708238 3.320000e-37 167.0
33 TraesCS5D01G084800 chr2B 88.430 121 12 2 5226 5345 575828172 575828053 1.560000e-30 145.0
34 TraesCS5D01G084800 chr7A 74.291 564 114 19 115 668 504226056 504225514 5.450000e-50 209.0
35 TraesCS5D01G084800 chr3A 92.647 136 10 0 3177 3312 34532615 34532480 4.240000e-46 196.0
36 TraesCS5D01G084800 chr1D 93.846 130 8 0 3177 3306 175820002 175819873 4.240000e-46 196.0
37 TraesCS5D01G084800 chr6D 91.912 136 11 0 3177 3312 304099286 304099421 1.970000e-44 191.0
38 TraesCS5D01G084800 chr2A 89.831 118 11 1 1654 1771 634598169 634598285 3.350000e-32 150.0
39 TraesCS5D01G084800 chr4D 89.076 119 10 3 5229 5345 311274756 311274873 1.560000e-30 145.0
40 TraesCS5D01G084800 chr1A 88.235 119 12 2 5228 5345 82355200 82355083 2.010000e-29 141.0
41 TraesCS5D01G084800 chr1A 90.291 103 10 0 1548 1650 590838825 590838723 9.370000e-28 135.0


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 TraesCS5D01G084800 chr5D 88874900 88880265 5365 True 9910.000000 9910 100.000000 1 5366 1 chr5D.!!$R2 5365
1 TraesCS5D01G084800 chr5A 82867954 82872455 4501 True 3554.650000 7014 93.890500 701 5231 2 chr5A.!!$R1 4530
2 TraesCS5D01G084800 chr5B 95511977 95516676 4699 False 2543.333333 5177 94.681333 698 5350 3 chr5B.!!$F2 4652
3 TraesCS5D01G084800 chr5B 53664967 53665538 571 False 678.000000 678 88.356000 2537 3107 1 chr5B.!!$F1 570
4 TraesCS5D01G084800 chr7D 478798923 478799469 546 True 595.000000 595 86.339000 3 549 1 chr7D.!!$R2 546
5 TraesCS5D01G084800 chr7D 636717084 636717757 673 False 531.000000 531 81.304000 24 698 1 chr7D.!!$F1 674
6 TraesCS5D01G084800 chr3B 708392116 708392660 544 False 595.000000 595 86.472000 3 546 1 chr3B.!!$F2 543
7 TraesCS5D01G084800 chr7B 739379395 739379942 547 True 590.000000 590 86.182000 3 549 1 chr7B.!!$R3 546
8 TraesCS5D01G084800 chr7B 707963137 707963846 709 True 523.000000 523 80.392000 3 698 1 chr7B.!!$R2 695
9 TraesCS5D01G084800 chr4A 58720353 58720871 518 True 584.000000 584 87.170000 2590 3110 1 chr4A.!!$R1 520
10 TraesCS5D01G084800 chr1B 94009232 94009779 547 True 579.000000 579 85.818000 3 549 1 chr1B.!!$R1 546
11 TraesCS5D01G084800 chr6B 706516529 706517237 708 True 534.000000 534 80.699000 3 699 1 chr6B.!!$R1 696
12 TraesCS5D01G084800 chr3D 489527699 489528376 677 False 523.000000 523 81.124000 24 698 1 chr3D.!!$F2 674
13 TraesCS5D01G084800 chr3D 614468970 614469664 694 True 520.000000 520 80.456000 3 691 1 chr3D.!!$R2 688
14 TraesCS5D01G084800 chr7A 504225514 504226056 542 True 209.000000 209 74.291000 115 668 1 chr7A.!!$R1 553


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
282 299 0.174162 GGTTCATGGTTGATGGCTGC 59.826 55.0 0.0 0.0 32.26 5.25 F
1356 1402 0.030638 GTGCAACTCCGCAACACAAT 59.969 50.0 0.0 0.0 45.14 2.71 F
1754 1809 0.608035 TTTCGGGCATGTTGGGTCTC 60.608 55.0 0.0 0.0 0.00 3.36 F
3321 3488 1.244019 CCCAACTTGTAGCACTGGGC 61.244 60.0 0.0 0.0 40.37 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1809 1.469940 CGGAACTGATCAGACGGAAGG 60.470 57.143 29.27 7.46 0.00 3.46 R
2989 3141 1.525175 ATCCCGAGGTAGGAGAGACT 58.475 55.000 0.00 0.00 36.67 3.24 R
3633 3817 1.571955 TCATGTAGCTCCTGCAGGAA 58.428 50.000 34.30 20.92 44.91 3.36 R
4978 5170 0.961019 TGCGCAAGATGAAAAGGCTT 59.039 45.000 8.16 0.00 43.02 4.35 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
65 66 3.574396 GAGGTGATCGGTCCTATGATTGA 59.426 47.826 0.00 0.00 33.83 2.57
71 72 3.576861 TCGGTCCTATGATTGAGGATGT 58.423 45.455 0.00 0.00 44.89 3.06
72 73 3.967326 TCGGTCCTATGATTGAGGATGTT 59.033 43.478 0.00 0.00 44.89 2.71
77 78 6.603201 GGTCCTATGATTGAGGATGTTTTTGA 59.397 38.462 0.00 0.00 44.89 2.69
80 81 9.258629 TCCTATGATTGAGGATGTTTTTGAAAT 57.741 29.630 0.00 0.00 38.22 2.17
97 99 7.873719 TTTGAAATCCAGTCTGTTCAAGTAA 57.126 32.000 13.67 2.12 40.14 2.24
168 170 1.463056 TCCATCGTTGCGACAACATTC 59.537 47.619 18.32 0.00 39.18 2.67
176 178 3.122150 CGACAACATTCGCTCCAGA 57.878 52.632 0.00 0.00 31.03 3.86
201 205 1.000955 CGTGGAGCTTGTGAGGTAGTT 59.999 52.381 0.00 0.00 32.79 2.24
224 229 2.056481 GAGCGGATGCAGATTGTGGC 62.056 60.000 0.00 0.00 46.23 5.01
274 291 1.580942 CGTGCTGGGTTCATGGTTG 59.419 57.895 0.00 0.00 0.00 3.77
282 299 0.174162 GGTTCATGGTTGATGGCTGC 59.826 55.000 0.00 0.00 32.26 5.25
321 339 1.340248 CTGTGTCTTAGTCGTGGTGGT 59.660 52.381 0.00 0.00 0.00 4.16
325 343 1.068127 GTCTTAGTCGTGGTGGTGTGT 59.932 52.381 0.00 0.00 0.00 3.72
334 352 1.344438 GTGGTGGTGTGTCAGATCTGA 59.656 52.381 21.67 21.67 37.24 3.27
377 395 2.202892 GCCCCGGTCTGATTCGTC 60.203 66.667 0.00 0.00 0.00 4.20
438 459 3.012518 GTCCACAAAGCTGCATATCAGT 58.987 45.455 1.02 0.00 44.66 3.41
445 466 3.851458 AGCTGCATATCAGTGATGGAA 57.149 42.857 16.15 1.69 44.66 3.53
455 476 0.677288 AGTGATGGAACCGTGTCGAA 59.323 50.000 0.00 0.00 0.00 3.71
533 556 2.297315 AGAAGCAGATGACGAGTGTTGA 59.703 45.455 0.00 0.00 0.00 3.18
537 560 2.738846 GCAGATGACGAGTGTTGATGTT 59.261 45.455 0.00 0.00 0.00 2.71
538 561 3.181526 GCAGATGACGAGTGTTGATGTTC 60.182 47.826 0.00 0.00 0.00 3.18
549 573 2.289882 TGTTGATGTTCAGCTCAGGGAG 60.290 50.000 0.00 0.00 0.00 4.30
587 611 8.644374 ATTGTATTTTTACTTCTTGGCTGGTA 57.356 30.769 0.00 0.00 0.00 3.25
590 614 6.575162 ATTTTTACTTCTTGGCTGGTAGTG 57.425 37.500 0.00 0.00 0.00 2.74
591 615 4.699925 TTTACTTCTTGGCTGGTAGTGT 57.300 40.909 0.00 0.00 0.00 3.55
602 626 3.492482 GGCTGGTAGTGTTTTGTGCAAAT 60.492 43.478 0.00 0.00 0.00 2.32
621 645 5.179368 GCAAATGCTAGTGTTCTGTTGTCTA 59.821 40.000 0.00 0.00 38.21 2.59
663 699 9.701098 TTGATTATTACGTGACTTGTACTCTTT 57.299 29.630 0.00 0.00 0.00 2.52
1011 1047 2.107750 CCGCACATGCCGATCTCT 59.892 61.111 7.82 0.00 37.91 3.10
1356 1402 0.030638 GTGCAACTCCGCAACACAAT 59.969 50.000 0.00 0.00 45.14 2.71
1526 1581 5.130350 CCTTCCACTGGAAAAAGTTACTCA 58.870 41.667 11.77 0.00 41.54 3.41
1613 1668 4.587891 TGATGCTGTTCATTACCATGACA 58.412 39.130 0.00 0.00 39.28 3.58
1754 1809 0.608035 TTTCGGGCATGTTGGGTCTC 60.608 55.000 0.00 0.00 0.00 3.36
1867 1922 6.512415 GCTTTTCTCCTGAATCATACCATTCG 60.512 42.308 0.00 0.00 35.78 3.34
1994 2125 4.100498 TGGAATCTAGGTCAACCCGTTATC 59.900 45.833 0.00 0.00 38.74 1.75
2068 2199 7.374272 TGTAGCATGCTCTTATTATCTCTGTC 58.626 38.462 26.57 0.00 0.00 3.51
2177 2312 4.929819 ACATGTTTTAAGGGTGTGAACC 57.070 40.909 0.00 0.00 0.00 3.62
2198 2333 6.773976 ACCATAAAATCCGATTCATGTTGT 57.226 33.333 11.76 4.58 0.00 3.32
2374 2509 2.686915 AGCAGATCAAAACATGCTAGCC 59.313 45.455 13.29 0.00 46.70 3.93
2989 3141 3.964688 TCCAACTGTTTCACTACCTCTCA 59.035 43.478 0.00 0.00 0.00 3.27
3321 3488 1.244019 CCCAACTTGTAGCACTGGGC 61.244 60.000 0.00 0.00 40.37 5.36
3464 3635 3.401182 TCAAAGCCATGGTGCATTTTTC 58.599 40.909 14.67 0.00 0.00 2.29
3488 3659 6.038382 TCGCACAGTTACCTTTTTGTATCAAA 59.962 34.615 0.00 0.00 0.00 2.69
3544 3715 5.012046 TGAGGTCATCTTACTTTCTTCAGCA 59.988 40.000 0.00 0.00 0.00 4.41
3776 3960 9.092876 GTTTGTTCTATCTCCTACTTCTTCATG 57.907 37.037 0.00 0.00 0.00 3.07
3807 3991 5.904362 ATATGTTTCCTCTTGTTTCTGCC 57.096 39.130 0.00 0.00 0.00 4.85
3910 4094 3.213206 TGTGTCTGATTTGAGCCACTT 57.787 42.857 0.00 0.00 0.00 3.16
4147 4331 3.454858 TCAGCCCCTCATATCTATTCCC 58.545 50.000 0.00 0.00 0.00 3.97
4951 5143 3.528597 TTTTGTTTTCGTTTCCCAGGG 57.471 42.857 0.00 0.00 0.00 4.45
4972 5164 3.526534 GTCAGAGACCATCCTTTAGTGC 58.473 50.000 0.00 0.00 0.00 4.40
4973 5165 2.501723 TCAGAGACCATCCTTTAGTGCC 59.498 50.000 0.00 0.00 0.00 5.01
4974 5166 2.503356 CAGAGACCATCCTTTAGTGCCT 59.497 50.000 0.00 0.00 0.00 4.75
4975 5167 2.503356 AGAGACCATCCTTTAGTGCCTG 59.497 50.000 0.00 0.00 0.00 4.85
4976 5168 1.561542 AGACCATCCTTTAGTGCCTGG 59.438 52.381 0.00 0.00 0.00 4.45
4977 5169 1.559682 GACCATCCTTTAGTGCCTGGA 59.440 52.381 0.00 0.00 0.00 3.86
4978 5170 1.992557 ACCATCCTTTAGTGCCTGGAA 59.007 47.619 0.00 0.00 31.87 3.53
4979 5171 2.378547 ACCATCCTTTAGTGCCTGGAAA 59.621 45.455 0.00 0.00 31.87 3.13
4995 5187 2.030007 TGGAAAGCCTTTTCATCTTGCG 60.030 45.455 0.00 0.00 43.62 4.85
5142 5337 7.899973 AGGATTGTGAGCAACTTGAATTTTAT 58.100 30.769 0.00 0.00 37.44 1.40
5151 5346 7.678837 AGCAACTTGAATTTTATGGAATTGGA 58.321 30.769 0.00 0.00 29.75 3.53
5163 5358 9.790344 TTTTATGGAATTGGATGTTTGATTTGT 57.210 25.926 0.00 0.00 0.00 2.83
5169 5364 8.260114 GGAATTGGATGTTTGATTTGTAGGAAT 58.740 33.333 0.00 0.00 0.00 3.01
5242 5437 5.306419 AGGTAAGATTATACCCCCTTCGTTC 59.694 44.000 0.01 0.00 45.42 3.95
5253 5448 6.579850 ACCCCCTTCGTTCCTTTATATAAA 57.420 37.500 7.66 7.66 0.00 1.40
5317 5513 9.038803 GCATTTCTTTCAATTCCTCATAATTCC 57.961 33.333 0.00 0.00 0.00 3.01
5321 5517 8.297470 TCTTTCAATTCCTCATAATTCCCTTG 57.703 34.615 0.00 0.00 0.00 3.61
5331 5527 5.837829 TCATAATTCCCTTGTTAGCCCTTT 58.162 37.500 0.00 0.00 0.00 3.11
5332 5528 6.260663 TCATAATTCCCTTGTTAGCCCTTTT 58.739 36.000 0.00 0.00 0.00 2.27
5333 5529 7.415086 TCATAATTCCCTTGTTAGCCCTTTTA 58.585 34.615 0.00 0.00 0.00 1.52
5334 5530 7.559897 TCATAATTCCCTTGTTAGCCCTTTTAG 59.440 37.037 0.00 0.00 0.00 1.85
5341 5537 6.455647 CCTTGTTAGCCCTTTTAGAAAAAGG 58.544 40.000 19.74 19.74 44.90 3.11
5359 5555 9.317936 AGAAAAAGGAAAACATCAACATCTTTC 57.682 29.630 0.00 0.00 0.00 2.62
5360 5556 9.317936 GAAAAAGGAAAACATCAACATCTTTCT 57.682 29.630 0.00 0.00 0.00 2.52
5361 5557 9.671279 AAAAAGGAAAACATCAACATCTTTCTT 57.329 25.926 0.00 0.00 0.00 2.52
5362 5558 8.877808 AAAGGAAAACATCAACATCTTTCTTC 57.122 30.769 0.00 0.00 0.00 2.87
5363 5559 7.830099 AGGAAAACATCAACATCTTTCTTCT 57.170 32.000 0.00 0.00 0.00 2.85
5364 5560 7.655490 AGGAAAACATCAACATCTTTCTTCTG 58.345 34.615 0.00 0.00 0.00 3.02
5365 5561 7.503566 AGGAAAACATCAACATCTTTCTTCTGA 59.496 33.333 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.478877 GGTAGGATCTGAAGAGACTTTATTCAA 58.521 37.037 0.00 0.00 32.87 2.69
22 23 2.366640 TCGGGGTAGGATCTGAAGAG 57.633 55.000 0.00 0.00 0.00 2.85
65 66 5.835280 ACAGACTGGATTTCAAAAACATCCT 59.165 36.000 7.51 0.00 37.88 3.24
71 72 7.169158 ACTTGAACAGACTGGATTTCAAAAA 57.831 32.000 16.21 1.24 37.48 1.94
72 73 6.773976 ACTTGAACAGACTGGATTTCAAAA 57.226 33.333 16.21 1.77 37.48 2.44
77 78 6.187727 TCCTTACTTGAACAGACTGGATTT 57.812 37.500 7.51 0.00 0.00 2.17
80 81 4.020218 CCATCCTTACTTGAACAGACTGGA 60.020 45.833 7.51 0.00 0.00 3.86
146 148 0.032815 TGTTGTCGCAACGATGGAGA 59.967 50.000 14.86 0.00 38.42 3.71
192 196 0.039180 TCCGCTCCTGAACTACCTCA 59.961 55.000 0.00 0.00 0.00 3.86
201 205 0.179065 CAATCTGCATCCGCTCCTGA 60.179 55.000 0.00 0.00 39.64 3.86
224 229 2.884827 TCAGATGTCGTTGATGCAGAG 58.115 47.619 0.00 0.00 0.00 3.35
256 273 0.888736 TCAACCATGAACCCAGCACG 60.889 55.000 0.00 0.00 30.99 5.34
274 291 4.488790 CCATACCTGGCAGCCATC 57.511 61.111 16.64 0.00 35.23 3.51
302 320 1.067974 CACCACCACGACTAAGACACA 59.932 52.381 0.00 0.00 0.00 3.72
321 339 4.488879 CATCGAACTTCAGATCTGACACA 58.511 43.478 25.07 10.08 39.66 3.72
325 343 2.480244 CGCCATCGAACTTCAGATCTGA 60.480 50.000 21.67 21.67 38.10 3.27
334 352 1.736645 CGGACACGCCATCGAACTT 60.737 57.895 0.00 0.00 39.41 2.66
377 395 1.238439 AGTGAAGCCATTGTCGTTGG 58.762 50.000 0.00 0.00 37.31 3.77
413 434 1.708341 ATGCAGCTTTGTGGACCTTT 58.292 45.000 0.00 0.00 0.00 3.11
438 459 2.465860 AATTCGACACGGTTCCATCA 57.534 45.000 0.00 0.00 0.00 3.07
445 466 0.107081 TCACCCAAATTCGACACGGT 59.893 50.000 0.00 0.00 0.00 4.83
455 476 1.566231 GGATCACCTCCTCACCCAAAT 59.434 52.381 0.00 0.00 41.29 2.32
494 517 3.289834 GGCACCACCACAGCAGTG 61.290 66.667 1.56 1.56 45.47 3.66
495 518 3.779850 CTGGCACCACCACAGCAGT 62.780 63.158 0.00 0.00 46.36 4.40
533 556 1.949799 AGACTCCCTGAGCTGAACAT 58.050 50.000 0.00 0.00 32.04 2.71
537 560 2.015456 TTGAAGACTCCCTGAGCTGA 57.985 50.000 0.00 0.00 32.04 4.26
538 561 2.419851 GGATTGAAGACTCCCTGAGCTG 60.420 54.545 0.00 0.00 32.04 4.24
587 611 4.142182 ACACTAGCATTTGCACAAAACACT 60.142 37.500 5.20 1.33 45.16 3.55
590 614 5.043248 AGAACACTAGCATTTGCACAAAAC 58.957 37.500 5.20 0.00 45.16 2.43
591 615 5.042593 CAGAACACTAGCATTTGCACAAAA 58.957 37.500 5.20 0.00 45.16 2.44
602 626 9.502091 AATTAAATAGACAACAGAACACTAGCA 57.498 29.630 0.00 0.00 0.00 3.49
631 655 8.492673 ACAAGTCACGTAATAATCAACATGAT 57.507 30.769 0.00 0.00 39.09 2.45
663 699 9.936759 TGGTAATACGCATCTCATTCATATAAA 57.063 29.630 0.00 0.00 0.00 1.40
699 735 1.373246 TACCGCGGCACACTGTAAC 60.373 57.895 28.58 0.00 0.00 2.50
1324 1370 4.494690 CGGAGTTGCACACATGATTATGAC 60.495 45.833 4.20 0.00 37.73 3.06
1362 1408 5.404096 TCTGTCTGCACGATCGTATTTTAA 58.596 37.500 22.26 5.10 0.00 1.52
1363 1409 4.989044 TCTGTCTGCACGATCGTATTTTA 58.011 39.130 22.26 5.35 0.00 1.52
1526 1581 9.833917 TTCTAGTACATCGATTCGATAGGATAT 57.166 33.333 20.34 8.18 45.19 1.63
1583 1638 5.817296 GGTAATGAACAGCATCAGTACATCA 59.183 40.000 19.34 2.24 46.99 3.07
1613 1668 3.980646 TTCTGCAAACAATACAAGCGT 57.019 38.095 0.00 0.00 0.00 5.07
1754 1809 1.469940 CGGAACTGATCAGACGGAAGG 60.470 57.143 29.27 7.46 0.00 3.46
1994 2125 2.938956 ACTTTTCCAGTCCACCTCAG 57.061 50.000 0.00 0.00 0.00 3.35
2068 2199 6.090898 AGTGACGTTGAATTTCGATTTCCTAG 59.909 38.462 0.00 0.00 0.00 3.02
2198 2333 8.842358 AAAATCGGACACTCAAAGAAACTATA 57.158 30.769 0.00 0.00 0.00 1.31
2340 2475 4.696899 TGATCTGCTGCTTCTCAAATTG 57.303 40.909 0.00 0.00 0.00 2.32
2440 2575 8.897872 TTTCGATCCTTTTCTTACTAACAACT 57.102 30.769 0.00 0.00 0.00 3.16
2457 2592 6.612306 AGTGAATAAAGCAAGTTTTCGATCC 58.388 36.000 0.00 0.00 0.00 3.36
2989 3141 1.525175 ATCCCGAGGTAGGAGAGACT 58.475 55.000 0.00 0.00 36.67 3.24
3488 3659 6.547510 ACAGAAACTAGCCTTCTTGTGAATTT 59.452 34.615 5.19 0.00 30.58 1.82
3633 3817 1.571955 TCATGTAGCTCCTGCAGGAA 58.428 50.000 34.30 20.92 44.91 3.36
3719 3903 7.561356 TCAGGTGATAATGATCTCAAGTAGTCA 59.439 37.037 0.00 0.00 32.79 3.41
3776 3960 5.355350 ACAAGAGGAAACATATTACTGCTGC 59.645 40.000 0.00 0.00 0.00 5.25
3807 3991 5.590530 AAGAAGCACTGGATAGACTACAG 57.409 43.478 0.00 0.00 38.19 2.74
3855 4039 2.418746 GCGAACCTGAGAAGCTTATCCA 60.419 50.000 18.02 6.67 0.00 3.41
4071 4255 0.764890 GTCATCATCCCCATTCCCGA 59.235 55.000 0.00 0.00 0.00 5.14
4147 4331 3.341043 CGCGCAAGATGATCCCGG 61.341 66.667 8.75 0.00 43.02 5.73
4951 5143 3.526534 GCACTAAAGGATGGTCTCTGAC 58.473 50.000 0.00 0.00 0.00 3.51
4971 5163 2.174360 AGATGAAAAGGCTTTCCAGGC 58.826 47.619 13.76 3.37 46.34 4.85
4972 5164 3.615834 GCAAGATGAAAAGGCTTTCCAGG 60.616 47.826 13.76 0.00 40.31 4.45
4973 5165 3.582780 GCAAGATGAAAAGGCTTTCCAG 58.417 45.455 13.76 0.00 40.31 3.86
4974 5166 2.030007 CGCAAGATGAAAAGGCTTTCCA 60.030 45.455 13.76 7.26 39.29 3.53
4975 5167 2.599659 CGCAAGATGAAAAGGCTTTCC 58.400 47.619 13.76 0.00 39.29 3.13
4976 5168 1.988467 GCGCAAGATGAAAAGGCTTTC 59.012 47.619 13.76 7.62 40.04 2.62
4977 5169 1.340889 TGCGCAAGATGAAAAGGCTTT 59.659 42.857 8.16 6.68 43.02 3.51
4978 5170 0.961019 TGCGCAAGATGAAAAGGCTT 59.039 45.000 8.16 0.00 43.02 4.35
4979 5171 1.133790 GATGCGCAAGATGAAAAGGCT 59.866 47.619 17.11 0.00 43.02 4.58
4995 5187 1.136147 CGCTCAAGCTTGGTGATGC 59.864 57.895 25.73 18.90 39.32 3.91
5039 5231 5.943416 ACGATGAAGGAAACCATACAAATCA 59.057 36.000 0.00 0.00 0.00 2.57
5142 5337 6.723515 TCCTACAAATCAAACATCCAATTCCA 59.276 34.615 0.00 0.00 0.00 3.53
5284 5480 7.178983 TGAGGAATTGAAAGAAATGCACCTTAT 59.821 33.333 0.00 0.00 0.00 1.73
5292 5488 9.538508 GGGAATTATGAGGAATTGAAAGAAATG 57.461 33.333 0.00 0.00 0.00 2.32
5300 5496 7.285401 GCTAACAAGGGAATTATGAGGAATTGA 59.715 37.037 0.00 0.00 0.00 2.57
5301 5497 7.428826 GCTAACAAGGGAATTATGAGGAATTG 58.571 38.462 0.00 0.00 0.00 2.32
5317 5513 6.266786 TCCTTTTTCTAAAAGGGCTAACAAGG 59.733 38.462 23.59 8.78 45.26 3.61
5321 5517 7.982919 TGTTTTCCTTTTTCTAAAAGGGCTAAC 59.017 33.333 23.59 22.07 45.26 2.34
5333 5529 9.317936 GAAAGATGTTGATGTTTTCCTTTTTCT 57.682 29.630 0.00 0.00 0.00 2.52
5334 5530 9.317936 AGAAAGATGTTGATGTTTTCCTTTTTC 57.682 29.630 0.00 0.00 0.00 2.29



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

AutoCloner maintained by Alex Coulton.