Multiple sequence alignment - TraesCS3D01G217100

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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 TraesCS3D01G217100 chr3D 100.000 6924 0 0 899 7822 294731718 294738641 0.000000e+00 12787.0
1 TraesCS3D01G217100 chr3D 100.000 452 0 0 1 452 294730820 294731271 0.000000e+00 835.0
2 TraesCS3D01G217100 chr3B 94.664 4048 132 21 899 4881 389037175 389041203 0.000000e+00 6202.0
3 TraesCS3D01G217100 chr3B 95.404 2959 109 13 4865 7811 389042171 389045114 0.000000e+00 4686.0
4 TraesCS3D01G217100 chr3B 91.562 320 11 3 146 452 389036870 389037186 2.020000e-115 427.0
5 TraesCS3D01G217100 chr3B 92.000 50 3 1 7632 7681 597475668 597475716 1.410000e-07 69.4
6 TraesCS3D01G217100 chr3A 97.048 3320 74 12 4152 7470 390013244 390016540 0.000000e+00 5566.0
7 TraesCS3D01G217100 chr3A 95.366 2611 57 11 1486 4061 390010657 390013238 0.000000e+00 4093.0
8 TraesCS3D01G217100 chr3A 94.408 1234 37 9 1240 2461 547999366 548000579 0.000000e+00 1868.0
9 TraesCS3D01G217100 chr3A 96.965 593 14 2 899 1491 390009790 390010378 0.000000e+00 992.0
10 TraesCS3D01G217100 chr3A 92.140 458 21 9 1 452 390009353 390009801 3.980000e-177 632.0
11 TraesCS3D01G217100 chr3A 84.740 308 27 12 7467 7764 390016937 390017234 2.760000e-74 291.0
12 TraesCS3D01G217100 chr5A 93.598 1234 44 11 1240 2461 490520672 490519462 0.000000e+00 1808.0
13 TraesCS3D01G217100 chr4A 93.193 1234 51 9 1240 2461 435283895 435282683 0.000000e+00 1783.0
14 TraesCS3D01G217100 chr4A 88.594 377 22 12 1 372 481728770 481729130 9.320000e-119 438.0
15 TraesCS3D01G217100 chr6B 93.572 949 36 14 1604 2540 421316712 421317647 0.000000e+00 1391.0
16 TraesCS3D01G217100 chr6B 91.772 474 28 5 1240 1712 421316229 421316692 0.000000e+00 649.0
17 TraesCS3D01G217100 chr7D 80.916 131 24 1 5054 5184 468514095 468513966 1.390000e-17 102.0
18 TraesCS3D01G217100 chr7B 80.153 131 25 1 5054 5184 491922583 491922454 6.460000e-16 97.1
19 TraesCS3D01G217100 chr1D 88.136 59 6 1 7631 7689 326287775 326287718 1.410000e-07 69.4
20 TraesCS3D01G217100 chr1D 93.617 47 1 2 7636 7682 483051507 483051463 1.410000e-07 69.4
21 TraesCS3D01G217100 chr1D 93.617 47 1 2 7636 7682 488481894 488481850 1.410000e-07 69.4
22 TraesCS3D01G217100 chr1A 93.617 47 1 2 7636 7682 579754937 579754893 1.410000e-07 69.4
23 TraesCS3D01G217100 chr1A 89.091 55 5 1 7631 7685 412460435 412460382 5.070000e-07 67.6
24 TraesCS3D01G217100 chr1B 87.931 58 4 3 7631 7686 439847509 439847453 1.820000e-06 65.8


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 TraesCS3D01G217100 chr3D 294730820 294738641 7821 False 6811.000000 12787 100.000000 1 7822 2 chr3D.!!$F1 7821
1 TraesCS3D01G217100 chr3B 389036870 389045114 8244 False 3771.666667 6202 93.876667 146 7811 3 chr3B.!!$F2 7665
2 TraesCS3D01G217100 chr3A 390009353 390017234 7881 False 2314.800000 5566 93.251800 1 7764 5 chr3A.!!$F2 7763
3 TraesCS3D01G217100 chr3A 547999366 548000579 1213 False 1868.000000 1868 94.408000 1240 2461 1 chr3A.!!$F1 1221
4 TraesCS3D01G217100 chr5A 490519462 490520672 1210 True 1808.000000 1808 93.598000 1240 2461 1 chr5A.!!$R1 1221
5 TraesCS3D01G217100 chr4A 435282683 435283895 1212 True 1783.000000 1783 93.193000 1240 2461 1 chr4A.!!$R1 1221
6 TraesCS3D01G217100 chr6B 421316229 421317647 1418 False 1020.000000 1391 92.672000 1240 2540 2 chr6B.!!$F1 1300

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
439 459 2.125673 GTAGCACCGCACCATCGT 60.126 61.111 0.00 0.0 0.00 3.73 F
1322 1342 0.824109 TGTAGAGGTGCCTTCGGATG 59.176 55.000 0.00 0.0 0.00 3.51 F
2200 2664 0.176680 ATCTACTGCTTCAGTGGCGG 59.823 55.000 9.52 0.0 45.01 6.13 F
3178 3690 0.320421 GTCAACTGCTCCACGCCTTA 60.320 55.000 0.00 0.0 38.05 2.69 F
4041 4553 1.202758 TCACCCGAGTTGTTCTGCATT 60.203 47.619 0.00 0.0 0.00 3.56 F
4123 4641 3.127030 GTGGTTGGCTGTATGTTAGAAGC 59.873 47.826 0.00 0.0 34.86 3.86 F
5536 7039 2.294512 GCACTTCCCTTTGTTTCCTCAG 59.705 50.000 0.00 0.0 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 2665 0.107831 TTTGTTCTAGCACCGCCAGT 59.892 50.000 0.00 0.00 0.00 4.00 R
2203 2667 0.948678 GTTTTGTTCTAGCACCGCCA 59.051 50.000 0.00 0.00 0.00 5.69 R
3844 4356 1.359848 AGACTCTACGGCAATTTGCG 58.640 50.000 14.83 12.29 46.21 4.85 R
4924 6427 1.265905 CCTACAACCCGTGTTTGAAGC 59.734 52.381 0.00 0.00 41.98 3.86 R
5495 6998 0.565674 AGGGTGGGGGTCAACAAATT 59.434 50.000 0.00 0.00 33.91 1.82 R
5729 7232 2.644555 ATAGACACGGTGATGGCGCC 62.645 60.000 22.73 22.73 41.39 6.53 R
7237 8744 1.471676 CGGGAGGAATGAGAAAGGTCG 60.472 57.143 0.00 0.00 0.00 4.79 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 3.484649 GTGTATGTGCGTGACTTATACCG 59.515 47.826 0.00 0.00 0.00 4.02
118 125 8.825745 TGAAAGAAAAACACATAGCAATTTTCC 58.174 29.630 0.00 0.00 39.58 3.13
136 143 9.846248 CAATTTTCCTTTTATTTCGAGAGACAT 57.154 29.630 0.00 0.00 41.84 3.06
168 179 2.452813 CGACAACCCGATTGCTCCG 61.453 63.158 0.00 0.00 42.62 4.63
281 292 9.764363 ACTAAATCAGGAAACCATTTTCTTTTC 57.236 29.630 0.00 0.00 40.98 2.29
439 459 2.125673 GTAGCACCGCACCATCGT 60.126 61.111 0.00 0.00 0.00 3.73
1197 1217 1.762957 TGGTACCAGCTGGATCTTAGC 59.237 52.381 39.19 27.28 41.43 3.09
1315 1335 3.077556 CCCGCTGTAGAGGTGCCT 61.078 66.667 1.03 0.00 32.75 4.75
1316 1336 2.660064 CCCGCTGTAGAGGTGCCTT 61.660 63.158 1.03 0.00 32.75 4.35
1317 1337 1.153549 CCGCTGTAGAGGTGCCTTC 60.154 63.158 0.00 0.00 0.00 3.46
1318 1338 1.517257 CGCTGTAGAGGTGCCTTCG 60.517 63.158 0.00 0.00 0.00 3.79
1319 1339 1.153549 GCTGTAGAGGTGCCTTCGG 60.154 63.158 0.00 0.00 0.00 4.30
1320 1340 1.605058 GCTGTAGAGGTGCCTTCGGA 61.605 60.000 0.00 0.00 0.00 4.55
1321 1341 1.115467 CTGTAGAGGTGCCTTCGGAT 58.885 55.000 0.00 0.00 0.00 4.18
1322 1342 0.824109 TGTAGAGGTGCCTTCGGATG 59.176 55.000 0.00 0.00 0.00 3.51
1336 1364 1.202758 TCGGATGTCTTGTGCCAAAGT 60.203 47.619 0.00 0.00 0.00 2.66
1432 1460 3.735591 TGCTGTGTAGGTAGTTTTCACC 58.264 45.455 0.00 0.00 36.22 4.02
1495 1807 4.706962 AGTCAAGGTCTTTCCATTATTGGC 59.293 41.667 0.00 0.00 43.29 4.52
1557 1879 7.500892 CCATAAGTTGGGCTGTGTATATGTAAA 59.499 37.037 0.00 0.00 42.33 2.01
1799 2251 5.246656 TCATGTTTTTCAGGCAAAGATGGAT 59.753 36.000 5.66 0.00 36.19 3.41
1880 2332 8.746052 TTGATTATTGTTCGTCTATCCCAATT 57.254 30.769 0.00 0.00 0.00 2.32
2094 2558 4.154176 TGGTCTGTAGCACTAACACCTAA 58.846 43.478 0.00 0.00 0.00 2.69
2123 2587 8.920509 AACACAATCACTTAGTTTTGGTTAAC 57.079 30.769 0.00 0.00 0.00 2.01
2196 2660 4.814147 TGAGTCAATCTACTGCTTCAGTG 58.186 43.478 9.52 1.03 45.01 3.66
2197 2661 4.180057 GAGTCAATCTACTGCTTCAGTGG 58.820 47.826 9.52 6.84 45.01 4.00
2198 2662 2.675348 GTCAATCTACTGCTTCAGTGGC 59.325 50.000 9.52 0.00 45.01 5.01
2199 2663 1.662629 CAATCTACTGCTTCAGTGGCG 59.337 52.381 9.52 0.00 45.01 5.69
2200 2664 0.176680 ATCTACTGCTTCAGTGGCGG 59.823 55.000 9.52 0.00 45.01 6.13
2201 2665 0.898326 TCTACTGCTTCAGTGGCGGA 60.898 55.000 9.52 1.14 45.01 5.54
2202 2666 0.737715 CTACTGCTTCAGTGGCGGAC 60.738 60.000 9.52 0.00 45.01 4.79
2203 2667 1.185618 TACTGCTTCAGTGGCGGACT 61.186 55.000 9.52 0.00 45.01 3.85
2227 2691 1.269723 GGTGCTAGAACAAAACCCTGC 59.730 52.381 2.51 0.00 0.00 4.85
2440 2929 1.888512 TCCTGTTGCATCTTGGCTTTC 59.111 47.619 0.00 0.00 34.04 2.62
2562 3051 6.183360 CCAAACTATAGGCTGCCATAATATGC 60.183 42.308 22.65 0.00 0.00 3.14
2731 3221 7.658982 CAGATGCCAAAGATGTATGTACATAGT 59.341 37.037 15.93 7.99 46.20 2.12
2801 3313 2.091541 TCCGATGGCTGAACATTTTCC 58.908 47.619 0.00 0.00 0.00 3.13
3088 3600 1.071605 GCGCATCGTTTCTTCTGTCT 58.928 50.000 0.30 0.00 0.00 3.41
3178 3690 0.320421 GTCAACTGCTCCACGCCTTA 60.320 55.000 0.00 0.00 38.05 2.69
3186 3698 1.473434 GCTCCACGCCTTATAGCTTGT 60.473 52.381 0.00 0.00 30.45 3.16
3365 3877 4.951254 TCTCTGTGTGAATACGTTTTGGA 58.049 39.130 0.00 0.00 0.00 3.53
3425 3937 9.914834 TTACTTATTGGCATAGTAAGGTTCAAT 57.085 29.630 14.99 0.00 34.03 2.57
3844 4356 1.578206 GCCAGGAAACAAGTCTCGCC 61.578 60.000 0.00 0.00 0.00 5.54
3987 4499 5.394115 AAGTTGACTTGCAAACCTTACAAGG 60.394 40.000 6.46 6.46 44.01 3.61
4041 4553 1.202758 TCACCCGAGTTGTTCTGCATT 60.203 47.619 0.00 0.00 0.00 3.56
4123 4641 3.127030 GTGGTTGGCTGTATGTTAGAAGC 59.873 47.826 0.00 0.00 34.86 3.86
4129 4647 6.294361 TGGCTGTATGTTAGAAGCTAAAGA 57.706 37.500 0.00 0.00 35.93 2.52
4131 4649 7.165485 TGGCTGTATGTTAGAAGCTAAAGAAA 58.835 34.615 0.00 0.00 35.93 2.52
4256 4774 5.801947 GTGGTGCATGTCTGTTCATAAATTC 59.198 40.000 0.00 0.00 0.00 2.17
4257 4775 5.476254 TGGTGCATGTCTGTTCATAAATTCA 59.524 36.000 0.00 0.00 0.00 2.57
4259 4777 6.349611 GGTGCATGTCTGTTCATAAATTCACT 60.350 38.462 0.00 0.00 0.00 3.41
4262 4780 7.175467 TGCATGTCTGTTCATAAATTCACTTCT 59.825 33.333 0.00 0.00 0.00 2.85
4299 4818 5.977129 TGCACATAGTCTAACATGATGTACG 59.023 40.000 0.00 0.00 0.00 3.67
4474 4993 8.340618 TCATTCAGCTTAGCTAAAATCTGTTT 57.659 30.769 20.33 11.90 36.40 2.83
4581 5100 9.034544 CGGATAAATCTTTGGAATTTGGAAATC 57.965 33.333 0.00 0.00 0.00 2.17
4644 5163 3.181422 ACATGGAGGATCTCACCGGTATA 60.181 47.826 6.87 0.00 33.73 1.47
4791 5310 6.015095 TCCCATACAGCTATGATTGACTAGTG 60.015 42.308 0.00 0.00 32.66 2.74
4918 6421 6.438741 TGGTTTTAGGTGAAATGGATGCATAA 59.561 34.615 0.00 0.00 0.00 1.90
4924 6427 6.812998 AGGTGAAATGGATGCATAATTCTTG 58.187 36.000 0.00 0.00 0.00 3.02
5026 6529 6.208644 GTGACATCTGTTTGCTTAACATGTT 58.791 36.000 16.68 16.68 45.31 2.71
5039 6542 3.896648 AACATGTTTCTGGCAGTTACG 57.103 42.857 15.27 5.05 0.00 3.18
5205 6708 3.144506 ACTGTGAGCTTCCATTTGACTG 58.855 45.455 0.00 0.00 0.00 3.51
5276 6779 5.048504 ACAGTGGACATTGATTTGTTAGCAG 60.049 40.000 1.66 0.00 0.00 4.24
5536 7039 2.294512 GCACTTCCCTTTGTTTCCTCAG 59.705 50.000 0.00 0.00 0.00 3.35
5580 7083 5.125356 TGCATTGTAATCCCTGATACAGTG 58.875 41.667 4.63 4.63 34.60 3.66
5692 7195 8.932791 GGTGACCCTTTATATATACACAATTCG 58.067 37.037 9.73 0.00 0.00 3.34
5729 7232 8.667076 TCAATCATAGTCATACAATCACCAAG 57.333 34.615 0.00 0.00 0.00 3.61
5740 7243 3.443045 CACCAAGGCGCCATCACC 61.443 66.667 31.54 0.00 0.00 4.02
5751 7254 1.600663 CGCCATCACCGTGTCTATCTC 60.601 57.143 0.00 0.00 0.00 2.75
5880 7383 7.343574 TGTTATCTATCTGCAGTAACCCAGTAA 59.656 37.037 14.67 2.16 0.00 2.24
5896 7399 7.422465 ACCCAGTAACAATCATATTGCAAAT 57.578 32.000 1.71 0.00 0.00 2.32
5937 7440 7.644157 GCTTTTCCACGATTAGATTGTTTATCC 59.356 37.037 0.00 0.00 33.45 2.59
6429 7936 4.098044 AGTGTATGTTCGCTGCTACTATGT 59.902 41.667 0.00 0.00 0.00 2.29
6641 8148 3.006859 TGCTTAGTACTTGAGCTGCAGAA 59.993 43.478 20.43 1.40 37.32 3.02
6644 8151 1.974236 AGTACTTGAGCTGCAGAAGGT 59.026 47.619 20.43 10.94 40.07 3.50
6654 8161 3.385755 AGCTGCAGAAGGTTTTTCATTGT 59.614 39.130 20.43 0.00 30.45 2.71
7278 8785 1.002250 CGTCAGTACAGACACCGTGC 61.002 60.000 17.36 0.00 38.43 5.34
7279 8786 0.314302 GTCAGTACAGACACCGTGCT 59.686 55.000 13.07 0.00 38.40 4.40
7280 8787 1.538512 GTCAGTACAGACACCGTGCTA 59.461 52.381 13.07 0.00 38.40 3.49
7281 8788 1.538512 TCAGTACAGACACCGTGCTAC 59.461 52.381 0.00 0.00 0.00 3.58
7282 8789 1.540267 CAGTACAGACACCGTGCTACT 59.460 52.381 0.00 0.00 0.00 2.57
7283 8790 1.811359 AGTACAGACACCGTGCTACTC 59.189 52.381 0.00 0.00 0.00 2.59
7482 8989 9.903682 AATTAAATGCATTCCTATCTGAATTCG 57.096 29.630 13.38 0.00 32.71 3.34
7493 9397 7.042335 TCCTATCTGAATTCGAAAAGGAGTTC 58.958 38.462 19.22 0.57 34.37 3.01
7532 9436 3.644966 ATCCAAAAAGAGACCGGCATA 57.355 42.857 0.00 0.00 0.00 3.14
7534 9438 1.743394 CCAAAAAGAGACCGGCATACC 59.257 52.381 0.00 0.00 0.00 2.73
7573 9477 6.951198 AGATCAAGAGATTCTCATACCCGTAT 59.049 38.462 15.83 0.00 33.72 3.06
7628 9547 7.156673 ACAAAAAGGATGTCCAAGAAATGATG 58.843 34.615 1.30 0.00 38.89 3.07
7630 9549 6.923199 AAAGGATGTCCAAGAAATGATGTT 57.077 33.333 1.30 0.00 38.89 2.71
7634 9553 6.947733 AGGATGTCCAAGAAATGATGTTAACA 59.052 34.615 11.41 11.41 38.89 2.41
7639 9558 6.915843 GTCCAAGAAATGATGTTAACAACGTT 59.084 34.615 13.23 14.49 30.57 3.99
7641 9560 6.915300 CCAAGAAATGATGTTAACAACGTTGA 59.085 34.615 33.66 12.23 29.96 3.18
7642 9561 7.096640 CCAAGAAATGATGTTAACAACGTTGAC 60.097 37.037 33.66 21.36 29.96 3.18
7643 9562 7.022055 AGAAATGATGTTAACAACGTTGACA 57.978 32.000 33.66 25.91 29.96 3.58
7644 9563 7.648142 AGAAATGATGTTAACAACGTTGACAT 58.352 30.769 33.66 28.94 33.93 3.06
7667 9588 8.677300 ACATATGTGGTAAGCAATTCAAACTAG 58.323 33.333 7.78 0.00 0.00 2.57
7729 9651 8.829373 AAAGTTTTCTTATATGCAGGAAGGAT 57.171 30.769 0.00 0.00 39.48 3.24
7734 9656 6.499106 TCTTATATGCAGGAAGGATGACAA 57.501 37.500 0.00 0.00 0.00 3.18
7797 9719 1.792301 CCGTACGACAGAAGAGCGA 59.208 57.895 18.76 0.00 0.00 4.93
7799 9721 0.520827 CGTACGACAGAAGAGCGACC 60.521 60.000 10.44 0.00 0.00 4.79
7800 9722 0.520827 GTACGACAGAAGAGCGACCG 60.521 60.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.373527 AGTCACGCACATACACAAAACTA 58.626 39.130 0.00 0.00 0.00 2.24
37 38 3.202906 AGTCACGCACATACACAAAACT 58.797 40.909 0.00 0.00 0.00 2.66
38 39 3.602390 AGTCACGCACATACACAAAAC 57.398 42.857 0.00 0.00 0.00 2.43
42 43 4.426416 GGTATAAGTCACGCACATACACA 58.574 43.478 0.00 0.00 0.00 3.72
43 44 3.484649 CGGTATAAGTCACGCACATACAC 59.515 47.826 0.00 0.00 0.00 2.90
44 45 3.377798 TCGGTATAAGTCACGCACATACA 59.622 43.478 0.00 0.00 0.00 2.29
45 46 3.956233 TCGGTATAAGTCACGCACATAC 58.044 45.455 0.00 0.00 0.00 2.39
46 47 4.320714 GGATCGGTATAAGTCACGCACATA 60.321 45.833 0.00 0.00 0.00 2.29
47 48 3.552273 GGATCGGTATAAGTCACGCACAT 60.552 47.826 0.00 0.00 0.00 3.21
48 49 2.223641 GGATCGGTATAAGTCACGCACA 60.224 50.000 0.00 0.00 0.00 4.57
49 50 2.223641 TGGATCGGTATAAGTCACGCAC 60.224 50.000 0.00 0.00 0.00 5.34
50 51 2.025898 TGGATCGGTATAAGTCACGCA 58.974 47.619 0.00 0.00 0.00 5.24
51 52 2.787601 TGGATCGGTATAAGTCACGC 57.212 50.000 0.00 0.00 0.00 5.34
118 125 8.191446 TCCTCTGTATGTCTCTCGAAATAAAAG 58.809 37.037 0.00 0.00 0.00 2.27
136 143 2.611971 GGTTGTCGCATTGTCCTCTGTA 60.612 50.000 0.00 0.00 0.00 2.74
138 145 0.798776 GGTTGTCGCATTGTCCTCTG 59.201 55.000 0.00 0.00 0.00 3.35
168 179 2.073816 ACGACGAAAACATGGATGGAC 58.926 47.619 0.00 0.00 0.00 4.02
256 267 9.208022 GGAAAAGAAAATGGTTTCCTGATTTAG 57.792 33.333 7.07 0.00 44.57 1.85
281 292 2.682155 CGAGAGGGAAGGAAGAAAGG 57.318 55.000 0.00 0.00 0.00 3.11
972 992 4.585526 TGGATGGATCGGACGCGC 62.586 66.667 5.73 0.00 0.00 6.86
981 1001 0.398522 TCGTGTAGGGCTGGATGGAT 60.399 55.000 0.00 0.00 0.00 3.41
982 1002 0.398522 ATCGTGTAGGGCTGGATGGA 60.399 55.000 0.00 0.00 0.00 3.41
983 1003 0.250038 CATCGTGTAGGGCTGGATGG 60.250 60.000 0.00 0.00 32.79 3.51
984 1004 0.752658 TCATCGTGTAGGGCTGGATG 59.247 55.000 0.00 0.00 36.66 3.51
1197 1217 4.485554 CTCGGGAGCAGAGAAACG 57.514 61.111 0.00 0.00 37.93 3.60
1313 1333 0.321564 TGGCACAAGACATCCGAAGG 60.322 55.000 0.00 0.00 45.32 3.46
1336 1364 1.339631 CCCCAGTACCAAAGCATCGAA 60.340 52.381 0.00 0.00 0.00 3.71
1495 1807 5.767665 ACTCCTATATGACACACTGCTCTAG 59.232 44.000 0.00 0.00 0.00 2.43
1616 1938 2.148916 TTGTTCGACACTCGCTGAAT 57.851 45.000 0.00 0.00 40.21 2.57
1618 1940 1.000717 TGATTGTTCGACACTCGCTGA 60.001 47.619 0.00 0.00 40.21 4.26
1780 2232 3.614630 CGCATCCATCTTTGCCTGAAAAA 60.615 43.478 0.00 0.00 35.41 1.94
1799 2251 1.085893 CATACATGTTCCAGTGCGCA 58.914 50.000 5.66 5.66 0.00 6.09
1880 2332 1.202687 AGTGACACTGCAGCAAGCTAA 60.203 47.619 15.27 0.00 45.94 3.09
2198 2662 3.001902 TTCTAGCACCGCCAGTCCG 62.002 63.158 0.00 0.00 0.00 4.79
2199 2663 1.448013 GTTCTAGCACCGCCAGTCC 60.448 63.158 0.00 0.00 0.00 3.85
2200 2664 0.320421 TTGTTCTAGCACCGCCAGTC 60.320 55.000 0.00 0.00 0.00 3.51
2201 2665 0.107831 TTTGTTCTAGCACCGCCAGT 59.892 50.000 0.00 0.00 0.00 4.00
2202 2666 1.069227 GTTTTGTTCTAGCACCGCCAG 60.069 52.381 0.00 0.00 0.00 4.85
2203 2667 0.948678 GTTTTGTTCTAGCACCGCCA 59.051 50.000 0.00 0.00 0.00 5.69
2227 2691 2.673893 GCTTTTGTAGAAATTGGCCCCG 60.674 50.000 0.00 0.00 0.00 5.73
2440 2929 6.042143 ACAAGCACATAGAAAAACAAGGTTG 58.958 36.000 0.00 0.00 38.67 3.77
2602 3092 3.396560 TGATGTCAACTGCAGAGAACAG 58.603 45.455 23.35 3.19 41.08 3.16
2801 3313 3.676540 ACGTGCTAAACAAAAACAGACG 58.323 40.909 0.00 0.00 0.00 4.18
3088 3600 8.918961 AAAACTTGATCGTTTTGTCATTTGTA 57.081 26.923 9.74 0.00 43.34 2.41
3421 3933 9.985730 ATTAAGCACAAATTCTTTCTCAATTGA 57.014 25.926 8.12 8.12 0.00 2.57
3425 3937 9.467258 CTTCATTAAGCACAAATTCTTTCTCAA 57.533 29.630 0.00 0.00 0.00 3.02
3844 4356 1.359848 AGACTCTACGGCAATTTGCG 58.640 50.000 14.83 12.29 46.21 4.85
3987 4499 3.746492 ACTTCCAAAGTTAGCGTCATGAC 59.254 43.478 16.21 16.21 39.04 3.06
4061 4573 7.009540 CAGATGGAAGTCTCAAAACACAAAAAC 59.990 37.037 0.00 0.00 0.00 2.43
4185 4703 6.923928 TCATATCACTGCATGATTTTTCGA 57.076 33.333 14.20 0.00 46.54 3.71
4299 4818 4.219033 CAAGTCGGAAAACAAGCACATAC 58.781 43.478 0.00 0.00 0.00 2.39
4411 4930 7.980099 GTGCACAACAGTAAAGTATATACTCCT 59.020 37.037 15.72 9.32 34.99 3.69
4447 4966 8.517062 ACAGATTTTAGCTAAGCTGAATGAAT 57.483 30.769 26.36 14.41 42.58 2.57
4581 5100 6.592798 ACAATGTTGAAACTTTGATTGCTG 57.407 33.333 21.73 2.43 43.04 4.41
4644 5163 9.628500 AACTAAGAGTTTGTAGATTTGGAAGTT 57.372 29.630 0.00 0.00 34.11 2.66
4714 5233 8.402798 TGAGGCTATAAATGTTTTTGTTCTCA 57.597 30.769 0.00 0.00 0.00 3.27
4800 5319 5.233050 CACTTGTAGCTGCAGTATATGTCAC 59.767 44.000 16.64 2.85 0.00 3.67
4918 6421 2.306847 ACCCGTGTTTGAAGCAAGAAT 58.693 42.857 0.00 0.00 0.00 2.40
4924 6427 1.265905 CCTACAACCCGTGTTTGAAGC 59.734 52.381 0.00 0.00 41.98 3.86
5026 6529 5.766174 AGAATAAAAACCGTAACTGCCAGAA 59.234 36.000 0.00 0.00 0.00 3.02
5039 6542 7.970614 CCTCTGCAGATTTACAGAATAAAAACC 59.029 37.037 18.63 0.00 42.12 3.27
5416 6919 2.750166 AGTCATGTAGTCACGACTCAGG 59.250 50.000 2.26 4.34 42.30 3.86
5495 6998 0.565674 AGGGTGGGGGTCAACAAATT 59.434 50.000 0.00 0.00 33.91 1.82
5580 7083 7.958053 ACAGTAGACATGTTAACTTGGTTAC 57.042 36.000 21.54 20.15 0.00 2.50
5692 7195 7.312657 TGACTATGATTGATTTGTGAAGAGC 57.687 36.000 0.00 0.00 0.00 4.09
5729 7232 2.644555 ATAGACACGGTGATGGCGCC 62.645 60.000 22.73 22.73 41.39 6.53
5740 7243 7.987268 TTTAAGCATTACAGAGATAGACACG 57.013 36.000 0.00 0.00 0.00 4.49
5780 7283 5.591877 AGCTTCCATGATGAAATGAACTACC 59.408 40.000 0.00 0.00 0.00 3.18
5850 7353 6.702282 GGGTTACTGCAGATAGATAACACTTC 59.298 42.308 23.35 5.35 0.00 3.01
5854 7357 5.661312 ACTGGGTTACTGCAGATAGATAACA 59.339 40.000 23.35 7.69 0.00 2.41
5896 7399 6.293735 CGTGGAAAAGCACCAAAATAGAACTA 60.294 38.462 0.00 0.00 39.22 2.24
5937 7440 5.505181 AACATCCCATAGCTGTAATAGGG 57.495 43.478 0.00 0.00 37.65 3.53
6277 7780 3.125316 GCTGAAGGAACACAGATTAACGG 59.875 47.826 0.00 0.00 37.23 4.44
6429 7936 5.873712 ACAAACAATCAATTTCACAAGCACA 59.126 32.000 0.00 0.00 0.00 4.57
6676 8183 3.388024 GGTGTTCTCTGGACCTGCATATA 59.612 47.826 0.00 0.00 0.00 0.86
6677 8184 2.171448 GGTGTTCTCTGGACCTGCATAT 59.829 50.000 0.00 0.00 0.00 1.78
6687 8194 3.722147 CATCTATTCCGGTGTTCTCTGG 58.278 50.000 0.00 0.00 35.33 3.86
6830 8337 2.100605 ACTGTCCCTTCGCTCATTTC 57.899 50.000 0.00 0.00 0.00 2.17
7237 8744 1.471676 CGGGAGGAATGAGAAAGGTCG 60.472 57.143 0.00 0.00 0.00 4.79
7283 8790 6.219473 CAGTAGACAGCAGTTTCCATATAGG 58.781 44.000 0.00 0.00 39.47 2.57
7464 8971 6.260936 TCCTTTTCGAATTCAGATAGGAATGC 59.739 38.462 18.33 0.00 37.55 3.56
7542 9446 7.122650 GGTATGAGAATCTCTTGATCTCTAGGG 59.877 44.444 11.92 0.00 34.92 3.53
7543 9447 7.122650 GGGTATGAGAATCTCTTGATCTCTAGG 59.877 44.444 11.92 0.00 34.92 3.02
7573 9477 6.136155 TGATATAGTCAGTCCATCTTCCACA 58.864 40.000 0.00 0.00 31.80 4.17
7628 9547 5.992729 ACCACATATGTCAACGTTGTTAAC 58.007 37.500 26.47 18.12 0.00 2.01
7630 9549 6.128499 GCTTACCACATATGTCAACGTTGTTA 60.128 38.462 26.47 17.12 0.00 2.41
7634 9553 4.320023 TGCTTACCACATATGTCAACGTT 58.680 39.130 5.07 0.00 0.00 3.99
7639 9558 7.176515 AGTTTGAATTGCTTACCACATATGTCA 59.823 33.333 5.07 0.00 0.00 3.58
7641 9560 7.466746 AGTTTGAATTGCTTACCACATATGT 57.533 32.000 1.41 1.41 0.00 2.29
7642 9561 8.677300 ACTAGTTTGAATTGCTTACCACATATG 58.323 33.333 0.00 0.00 0.00 1.78
7643 9562 8.807948 ACTAGTTTGAATTGCTTACCACATAT 57.192 30.769 0.00 0.00 0.00 1.78
7644 9563 7.335924 GGACTAGTTTGAATTGCTTACCACATA 59.664 37.037 0.00 0.00 0.00 2.29
7667 9588 9.543018 CAGTCGTTTATATCTTTTCTTTTGGAC 57.457 33.333 0.00 0.00 0.00 4.02
7684 9605 0.881159 CCCACGCAACCAGTCGTTTA 60.881 55.000 0.00 0.00 36.73 2.01
7734 9656 5.768164 ACCTCGGTTTTGAAAATGTAGACAT 59.232 36.000 0.00 0.00 38.41 3.06
7773 9695 1.592400 CTTCTGTCGTACGGCCTCCA 61.592 60.000 18.57 0.00 0.00 3.86
7781 9703 0.520827 CGGTCGCTCTTCTGTCGTAC 60.521 60.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.