Multiple sequence alignment - TraesCS2D01G025100

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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 TraesCS2D01G025100 chr2D 100.000 3389 0 0 1 3389 10981975 10978587 0.000000e+00 6259.0
1 TraesCS2D01G025100 chr2D 73.724 529 108 17 1304 1821 570082032 570082540 9.660000e-41 178.0
2 TraesCS2D01G025100 chr2B 87.672 1744 142 23 719 2440 16773918 16772226 0.000000e+00 1962.0
3 TraesCS2D01G025100 chr2B 86.861 274 32 4 428 698 438614787 438614515 1.530000e-78 303.0
4 TraesCS2D01G025100 chr2B 74.359 390 73 16 1042 1407 13392195 13392581 1.270000e-29 141.0
5 TraesCS2D01G025100 chr2B 79.558 181 37 0 1227 1407 13219828 13220008 2.740000e-26 130.0
6 TraesCS2D01G025100 chr2B 90.217 92 6 1 957 1048 16788055 16787967 2.140000e-22 117.0
7 TraesCS2D01G025100 chr2A 93.581 888 52 3 1964 2846 11641440 11640553 0.000000e+00 1319.0
8 TraesCS2D01G025100 chr2A 91.924 681 43 5 1042 1714 11642114 11641438 0.000000e+00 942.0
9 TraesCS2D01G025100 chr2A 89.441 644 60 8 263 902 11657099 11656460 0.000000e+00 806.0
10 TraesCS2D01G025100 chr2A 89.535 602 55 6 3 598 11645425 11644826 0.000000e+00 756.0
11 TraesCS2D01G025100 chr2A 78.177 834 157 12 1552 2362 9124702 9125533 3.020000e-140 508.0
12 TraesCS2D01G025100 chr2A 89.751 361 28 3 587 938 11642607 11642247 1.430000e-123 453.0
13 TraesCS2D01G025100 chr2A 79.815 540 98 9 1834 2366 24149602 24149067 1.910000e-102 383.0
14 TraesCS2D01G025100 chr2A 91.852 270 9 3 1 268 11662558 11662300 6.910000e-97 364.0
15 TraesCS2D01G025100 chr2A 75.206 851 147 41 1042 1830 24150701 24149853 9.000000e-91 344.0
16 TraesCS2D01G025100 chr2A 90.040 251 24 1 436 685 575349283 575349033 1.170000e-84 324.0
17 TraesCS2D01G025100 chr3D 77.835 1164 206 27 1237 2365 464333401 464332255 0.000000e+00 673.0
18 TraesCS2D01G025100 chr3D 86.195 565 71 6 2830 3389 317211472 317210910 3.740000e-169 604.0
19 TraesCS2D01G025100 chr3D 74.946 1381 244 51 1043 2365 464720892 464719556 1.070000e-149 540.0
20 TraesCS2D01G025100 chr3A 76.386 1389 233 49 1044 2365 607509516 607508156 0.000000e+00 660.0
21 TraesCS2D01G025100 chr3A 76.522 690 117 24 1223 1885 608113461 608112790 5.420000e-88 335.0
22 TraesCS2D01G025100 chr3A 91.429 70 6 0 1052 1121 608118669 608118600 2.780000e-16 97.1
23 TraesCS2D01G025100 chr1D 86.258 604 75 5 2790 3389 339960865 339961464 0.000000e+00 649.0
24 TraesCS2D01G025100 chr1D 88.846 260 26 3 428 685 401204564 401204822 1.960000e-82 316.0
25 TraesCS2D01G025100 chr7D 75.997 1379 238 52 1041 2365 19399720 19401059 7.980000e-176 627.0
26 TraesCS2D01G025100 chr5D 84.333 600 89 5 2792 3387 207258100 207257502 1.750000e-162 582.0
27 TraesCS2D01G025100 chr5D 90.654 428 34 4 1 423 14081278 14080852 6.350000e-157 564.0
28 TraesCS2D01G025100 chrUn 84.106 604 91 4 2790 3389 154973556 154974158 2.270000e-161 579.0
29 TraesCS2D01G025100 chrUn 83.775 604 93 4 2790 3389 414146476 414145874 4.910000e-158 568.0
30 TraesCS2D01G025100 chrUn 86.946 406 53 0 1726 2131 478013392 478013797 1.110000e-124 457.0
31 TraesCS2D01G025100 chr3B 83.940 604 92 4 2790 3389 792320308 792319706 1.050000e-159 573.0
32 TraesCS2D01G025100 chr3B 83.775 604 93 4 2790 3389 792407122 792406520 4.910000e-158 568.0
33 TraesCS2D01G025100 chr3B 83.775 604 93 4 2790 3389 793419639 793420241 4.910000e-158 568.0
34 TraesCS2D01G025100 chr3B 79.302 831 149 14 1557 2365 618008402 618007573 8.210000e-156 560.0
35 TraesCS2D01G025100 chr3B 90.079 252 22 3 436 685 17707715 17707965 1.170000e-84 324.0
36 TraesCS2D01G025100 chr4A 83.609 604 94 4 2790 3389 717829290 717828688 2.280000e-156 562.0
37 TraesCS2D01G025100 chr7B 90.323 248 22 2 436 681 508192824 508193071 1.170000e-84 324.0
38 TraesCS2D01G025100 chr7B 89.453 256 24 3 431 684 254082196 254081942 1.520000e-83 320.0
39 TraesCS2D01G025100 chr7A 89.641 251 25 1 436 685 433739006 433739256 5.460000e-83 318.0
40 TraesCS2D01G025100 chr7A 80.928 194 37 0 1484 1677 677653834 677653641 1.630000e-33 154.0
41 TraesCS2D01G025100 chr6A 80.142 141 22 6 266 404 409384916 409384780 2.150000e-17 100.0


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 TraesCS2D01G025100 chr2D 10978587 10981975 3388 True 6259.0 6259 100.00000 1 3389 1 chr2D.!!$R1 3388
1 TraesCS2D01G025100 chr2B 16772226 16773918 1692 True 1962.0 1962 87.67200 719 2440 1 chr2B.!!$R1 1721
2 TraesCS2D01G025100 chr2A 11640553 11645425 4872 True 867.5 1319 91.19775 3 2846 4 chr2A.!!$R4 2843
3 TraesCS2D01G025100 chr2A 11656460 11657099 639 True 806.0 806 89.44100 263 902 1 chr2A.!!$R1 639
4 TraesCS2D01G025100 chr2A 9124702 9125533 831 False 508.0 508 78.17700 1552 2362 1 chr2A.!!$F1 810
5 TraesCS2D01G025100 chr2A 24149067 24150701 1634 True 363.5 383 77.51050 1042 2366 2 chr2A.!!$R5 1324
6 TraesCS2D01G025100 chr3D 464332255 464333401 1146 True 673.0 673 77.83500 1237 2365 1 chr3D.!!$R2 1128
7 TraesCS2D01G025100 chr3D 317210910 317211472 562 True 604.0 604 86.19500 2830 3389 1 chr3D.!!$R1 559
8 TraesCS2D01G025100 chr3D 464719556 464720892 1336 True 540.0 540 74.94600 1043 2365 1 chr3D.!!$R3 1322
9 TraesCS2D01G025100 chr3A 607508156 607509516 1360 True 660.0 660 76.38600 1044 2365 1 chr3A.!!$R1 1321
10 TraesCS2D01G025100 chr3A 608112790 608113461 671 True 335.0 335 76.52200 1223 1885 1 chr3A.!!$R2 662
11 TraesCS2D01G025100 chr1D 339960865 339961464 599 False 649.0 649 86.25800 2790 3389 1 chr1D.!!$F1 599
12 TraesCS2D01G025100 chr7D 19399720 19401059 1339 False 627.0 627 75.99700 1041 2365 1 chr7D.!!$F1 1324
13 TraesCS2D01G025100 chr5D 207257502 207258100 598 True 582.0 582 84.33300 2792 3387 1 chr5D.!!$R2 595
14 TraesCS2D01G025100 chrUn 154973556 154974158 602 False 579.0 579 84.10600 2790 3389 1 chrUn.!!$F1 599
15 TraesCS2D01G025100 chrUn 414145874 414146476 602 True 568.0 568 83.77500 2790 3389 1 chrUn.!!$R1 599
16 TraesCS2D01G025100 chr3B 792319706 792320308 602 True 573.0 573 83.94000 2790 3389 1 chr3B.!!$R2 599
17 TraesCS2D01G025100 chr3B 792406520 792407122 602 True 568.0 568 83.77500 2790 3389 1 chr3B.!!$R3 599
18 TraesCS2D01G025100 chr3B 793419639 793420241 602 False 568.0 568 83.77500 2790 3389 1 chr3B.!!$F2 599
19 TraesCS2D01G025100 chr3B 618007573 618008402 829 True 560.0 560 79.30200 1557 2365 1 chr3B.!!$R1 808
20 TraesCS2D01G025100 chr4A 717828688 717829290 602 True 562.0 562 83.60900 2790 3389 1 chr4A.!!$R1 599

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
252 257 0.033796 CCGTCCACCTCCTAGTACCA 60.034 60.000 0.00 0.00 0.0 3.25 F
255 260 1.008403 TCCACCTCCTAGTACCAGCT 58.992 55.000 0.00 0.00 0.0 4.24 F
256 261 1.115467 CCACCTCCTAGTACCAGCTG 58.885 60.000 6.78 6.78 0.0 4.24 F
2025 4715 1.007271 CGACTTCCTGACGCACTGT 60.007 57.895 0.00 0.00 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1456 3848 0.877213 GGCACGGATAATACGGCGTT 60.877 55.000 21.24 2.90 35.23 4.84 R
2009 4699 1.069765 CCACAGTGCGTCAGGAAGT 59.930 57.895 0.00 0.00 0.00 3.01 R
2214 4904 2.202878 ATCAATGTCCCGACGGCG 60.203 61.111 1.94 1.94 37.24 6.46 R
2950 5655 1.326548 GTACGCGGATTGTTTGGCTAG 59.673 52.381 12.47 0.00 0.00 3.42 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
17 18 4.136978 AGATCGGGCCAGTCAACT 57.863 55.556 4.39 0.00 0.00 3.16
85 86 1.664873 CTAGGGAGCGCCAGATCTG 59.335 63.158 16.24 16.24 35.15 2.90
106 107 1.075970 TGGAGGACTCGCCATAGCT 60.076 57.895 0.00 0.00 37.94 3.32
110 111 2.659897 GACTCGCCATAGCTGCCG 60.660 66.667 0.00 0.00 36.60 5.69
171 174 1.377333 GGCAAGGTACACTCAGCCC 60.377 63.158 12.68 0.00 41.77 5.19
197 200 0.256752 TGCATATCCAGCAAGCCAGT 59.743 50.000 0.00 0.00 39.39 4.00
216 219 1.899437 TAACCCGAGAGCCAAGCCAG 61.899 60.000 0.00 0.00 0.00 4.85
252 257 0.033796 CCGTCCACCTCCTAGTACCA 60.034 60.000 0.00 0.00 0.00 3.25
253 258 1.390565 CGTCCACCTCCTAGTACCAG 58.609 60.000 0.00 0.00 0.00 4.00
254 259 1.112950 GTCCACCTCCTAGTACCAGC 58.887 60.000 0.00 0.00 0.00 4.85
255 260 1.008403 TCCACCTCCTAGTACCAGCT 58.992 55.000 0.00 0.00 0.00 4.24
256 261 1.115467 CCACCTCCTAGTACCAGCTG 58.885 60.000 6.78 6.78 0.00 4.24
257 262 1.342076 CCACCTCCTAGTACCAGCTGA 60.342 57.143 17.39 0.00 0.00 4.26
258 263 1.751924 CACCTCCTAGTACCAGCTGAC 59.248 57.143 17.39 6.33 0.00 3.51
311 317 2.343758 GAGCTTCACTGGCCGACA 59.656 61.111 0.00 0.00 0.00 4.35
453 459 6.872020 TGTTTCATACTCCCTTCGTCTTTAAG 59.128 38.462 0.00 0.00 0.00 1.85
462 468 5.950549 TCCCTTCGTCTTTAAGAGAGTGTAT 59.049 40.000 0.00 0.00 34.31 2.29
474 480 5.948992 AGAGAGTGTATTTCCAACTTTGC 57.051 39.130 0.00 0.00 0.00 3.68
645 2883 9.734620 CACAAACTTGATCAAACTTTGAGATAA 57.265 29.630 28.64 4.64 43.98 1.75
688 2926 9.120538 AGTTGAAAGTACATTCTTTTAAGAGCA 57.879 29.630 11.75 0.00 37.70 4.26
698 2936 7.116519 ACATTCTTTTAAGAGCAGACGAAGTAC 59.883 37.037 0.00 0.00 37.30 2.73
797 3036 5.463724 GCGAATCTGAGGTAAAGTAGAATGG 59.536 44.000 0.00 0.00 0.00 3.16
961 3214 6.073327 TCCTTGAGCATGTACGTATAAGAG 57.927 41.667 0.00 0.00 0.00 2.85
1146 3484 1.153369 CCCACCAATCGACATCGCT 60.153 57.895 0.00 0.00 39.60 4.93
1175 3513 2.361357 CCCTGACGTCGGTCTCCT 60.361 66.667 22.45 0.00 43.79 3.69
1464 3856 2.580276 GGTGATCCCAACGCCGTA 59.420 61.111 0.00 0.00 0.00 4.02
1537 3944 3.948719 GGCACCCCGACCAGTTGA 61.949 66.667 0.00 0.00 0.00 3.18
1542 3949 1.227734 CCCCGACCAGTTGACGTTT 60.228 57.895 0.00 0.00 0.00 3.60
1721 4143 3.681835 GTCCAGAGGCACCGACGT 61.682 66.667 0.00 0.00 0.00 4.34
1962 4652 1.157870 CCCGTGGTTACATCATCCGC 61.158 60.000 0.00 0.00 0.00 5.54
2025 4715 1.007271 CGACTTCCTGACGCACTGT 60.007 57.895 0.00 0.00 0.00 3.55
2517 5219 2.674954 TGCCATGCTGAAAACGAAATG 58.325 42.857 0.00 0.00 0.00 2.32
2522 5225 1.000385 TGCTGAAAACGAAATGCCAGG 60.000 47.619 0.00 0.00 0.00 4.45
2588 5292 6.488344 TGGCAATTTAGCATGATACCGAAATA 59.512 34.615 0.00 0.00 35.83 1.40
2628 5332 6.490241 ACACCACTGGTACTAAAACTTAGT 57.510 37.500 0.00 4.59 32.11 2.24
2641 5345 8.585189 ACTAAAACTTAGTACGAAAAGTCAGG 57.415 34.615 10.45 5.99 34.91 3.86
2651 5355 4.304939 ACGAAAAGTCAGGTTAGTGCTAC 58.695 43.478 0.00 0.00 0.00 3.58
2653 5357 4.748102 CGAAAAGTCAGGTTAGTGCTACAA 59.252 41.667 0.00 0.00 0.00 2.41
2676 5380 4.263727 ACTTGGGCATACATTGAACTGGTA 60.264 41.667 0.00 0.00 0.00 3.25
2677 5381 4.308526 TGGGCATACATTGAACTGGTAA 57.691 40.909 0.00 0.00 0.00 2.85
2694 5398 5.061920 TGGTAACACAACTTGGTTTTGAC 57.938 39.130 3.99 0.00 46.17 3.18
2700 5404 2.165437 ACAACTTGGTTTTGACGTGCAT 59.835 40.909 0.00 0.00 0.00 3.96
2701 5405 2.490328 ACTTGGTTTTGACGTGCATG 57.510 45.000 3.82 3.82 0.00 4.06
2704 5408 3.242936 ACTTGGTTTTGACGTGCATGTAC 60.243 43.478 12.53 6.34 0.00 2.90
2736 5440 1.058129 CGTTTGTATACGACACGGTGC 59.942 52.381 8.30 0.19 43.99 5.01
2912 5617 6.961360 TTGTGAGTCTCCGATAATGTATCT 57.039 37.500 0.00 0.00 33.01 1.98
2938 5643 4.924625 TCCCCAAATAACTGATCGGAAAA 58.075 39.130 9.00 0.00 0.00 2.29
2950 5655 0.033894 TCGGAAAATGGCCTAACCCC 60.034 55.000 3.32 0.00 37.83 4.95
2951 5656 0.033503 CGGAAAATGGCCTAACCCCT 60.034 55.000 3.32 0.00 37.83 4.79
2964 5670 2.231716 AACCCCTAGCCAAACAATCC 57.768 50.000 0.00 0.00 0.00 3.01
3046 5755 2.735151 TCTTAAGACCCGAGAGATGCA 58.265 47.619 0.00 0.00 0.00 3.96
3048 5757 1.847328 TAAGACCCGAGAGATGCACA 58.153 50.000 0.00 0.00 0.00 4.57
3080 5789 7.444183 TGACAAAGTTAATTTCAGATTCCTCGT 59.556 33.333 0.00 0.00 0.00 4.18
3090 5799 6.835819 TTCAGATTCCTCGTTTTCTCTAGA 57.164 37.500 0.00 0.00 0.00 2.43
3115 5824 8.768957 ATCATGATCCATAAAGTGAATCGTAG 57.231 34.615 1.18 0.00 0.00 3.51
3134 5843 4.319766 CGTAGCATTGGCATATTGAAGGAC 60.320 45.833 0.00 0.00 44.61 3.85
3193 5902 4.321601 CGTCAATTTGGCCATCAACCTTTA 60.322 41.667 6.09 0.00 34.67 1.85
3197 5906 2.666272 TGGCCATCAACCTTTACACA 57.334 45.000 0.00 0.00 0.00 3.72
3224 5933 7.503549 TCAATCATGACAGCTAACATATCAGT 58.496 34.615 0.00 0.00 0.00 3.41
3232 5941 9.131791 TGACAGCTAACATATCAGTCACTATAA 57.868 33.333 0.00 0.00 30.43 0.98
3301 6010 0.887387 TTGGAAGTAGCGGCCAACAC 60.887 55.000 2.24 0.00 36.80 3.32
3328 6038 4.433186 TTGAATTTAATGGCCACACTCG 57.567 40.909 8.16 0.00 0.00 4.18
3330 6040 1.832883 ATTTAATGGCCACACTCGCA 58.167 45.000 8.16 0.00 0.00 5.10
3348 6058 2.346803 GCACCAGAAACGAAGCTATGA 58.653 47.619 0.00 0.00 0.00 2.15
3350 6060 3.424962 GCACCAGAAACGAAGCTATGAAC 60.425 47.826 0.00 0.00 0.00 3.18
3351 6061 2.993899 ACCAGAAACGAAGCTATGAACG 59.006 45.455 0.00 0.00 0.00 3.95
3356 6066 4.156190 AGAAACGAAGCTATGAACGAGAGA 59.844 41.667 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.115467 CTAGTTGACTGGCCCGATCT 58.885 55.000 0.00 0.00 0.00 2.75
1 2 0.105039 CCTAGTTGACTGGCCCGATC 59.895 60.000 0.00 0.00 0.00 3.69
17 18 1.301401 GTGTGGAGCACGTTGCCTA 60.301 57.895 6.39 0.00 46.52 3.93
25 26 0.460284 CTATCACGGGTGTGGAGCAC 60.460 60.000 0.00 0.00 46.42 4.40
37 38 2.607635 CCCAACGATGGTTTCTATCACG 59.392 50.000 11.15 0.00 46.01 4.35
85 86 1.749334 CTATGGCGAGTCCTCCACCC 61.749 65.000 1.24 0.00 34.81 4.61
88 89 1.075970 AGCTATGGCGAGTCCTCCA 60.076 57.895 0.00 1.69 44.37 3.86
120 121 4.787999 CCGCTCGGTGAAGACTAC 57.212 61.111 0.00 0.00 0.00 2.73
146 149 1.153429 GTGTACCTTGCCCGCTAGG 60.153 63.158 14.53 14.53 43.05 3.02
159 162 1.446272 GCGACAGGGCTGAGTGTAC 60.446 63.158 0.00 0.00 0.00 2.90
171 174 0.531311 TGCTGGATATGCAGCGACAG 60.531 55.000 34.70 9.27 46.60 3.51
197 200 1.899437 CTGGCTTGGCTCTCGGGTTA 61.899 60.000 0.00 0.00 0.00 2.85
216 219 3.044305 GCGTGCCTCTGGTGTGTC 61.044 66.667 0.00 0.00 0.00 3.67
235 240 1.112950 GCTGGTACTAGGAGGTGGAC 58.887 60.000 8.46 0.00 0.00 4.02
378 384 2.202676 GCTCTTCCTGGCGACTCG 60.203 66.667 0.00 0.00 0.00 4.18
453 459 5.335191 CCAGCAAAGTTGGAAATACACTCTC 60.335 44.000 0.00 0.00 37.96 3.20
645 2883 8.755028 ACTTTCAACTTTGTTGTAGGGTTAATT 58.245 29.630 9.78 0.00 0.00 1.40
646 2884 8.301252 ACTTTCAACTTTGTTGTAGGGTTAAT 57.699 30.769 9.78 0.00 0.00 1.40
649 2887 6.660094 TGTACTTTCAACTTTGTTGTAGGGTT 59.340 34.615 9.78 0.00 0.00 4.11
655 2893 9.705290 AAAAGAATGTACTTTCAACTTTGTTGT 57.295 25.926 20.10 0.82 38.86 3.32
686 2924 2.507866 GTTCTCTCGTACTTCGTCTGC 58.492 52.381 0.00 0.00 40.80 4.26
688 2926 1.731160 CCGTTCTCTCGTACTTCGTCT 59.269 52.381 0.00 0.00 40.80 4.18
698 2936 1.725066 GAGAGCCTCCGTTCTCTCG 59.275 63.158 3.85 0.00 43.80 4.04
797 3036 1.135286 GCAAGGATAACAGCTGCCAAC 60.135 52.381 15.27 3.25 0.00 3.77
947 3200 2.818432 CGGGCCTCTCTTATACGTACAT 59.182 50.000 0.84 0.00 0.00 2.29
1146 3484 1.070786 GTCAGGGAAAGGCACGACA 59.929 57.895 0.00 0.00 0.00 4.35
1281 3634 2.278013 GAGACCACGGCGTCGATC 60.278 66.667 20.03 10.91 37.85 3.69
1356 3709 4.379243 CTGGTGCCGAGGAACGCT 62.379 66.667 0.00 0.00 41.07 5.07
1414 3767 2.429739 GTCGTCGTCGGGGTTGTC 60.430 66.667 1.55 0.00 37.69 3.18
1436 3828 2.404995 GGATCACCCTCGTCGTCGT 61.405 63.158 1.33 0.00 38.33 4.34
1456 3848 0.877213 GGCACGGATAATACGGCGTT 60.877 55.000 21.24 2.90 35.23 4.84
1513 3908 2.668632 GTCGGGGTGCCTCATCAA 59.331 61.111 0.00 0.00 0.00 2.57
1537 3944 2.423577 GTAGATGCCCTTGACAAACGT 58.576 47.619 0.00 0.00 0.00 3.99
1542 3949 4.932789 GCGTAGATGCCCTTGACA 57.067 55.556 0.00 0.00 0.00 3.58
1613 4020 1.304630 TAGTGCTCCACGTAGCCCA 60.305 57.895 7.82 0.00 42.05 5.36
1737 4159 3.790437 CAGGGGATGCAGCCGTCT 61.790 66.667 16.15 12.29 0.00 4.18
1973 4663 5.514310 GGGTGGTTTAAGATGAGTACCTGTT 60.514 44.000 0.00 0.00 0.00 3.16
2009 4699 1.069765 CCACAGTGCGTCAGGAAGT 59.930 57.895 0.00 0.00 0.00 3.01
2025 4715 2.915659 AGCGTCGAGTTCCACCCA 60.916 61.111 0.00 0.00 0.00 4.51
2214 4904 2.202878 ATCAATGTCCCGACGGCG 60.203 61.111 1.94 1.94 37.24 6.46
2384 5086 1.429148 GCCGTCACCATCGAATCACC 61.429 60.000 0.00 0.00 0.00 4.02
2543 5247 6.101332 TGCCAATGCAGAAACATAATCTTTC 58.899 36.000 0.00 0.00 44.23 2.62
2545 5249 5.664294 TGCCAATGCAGAAACATAATCTT 57.336 34.783 0.00 0.00 44.23 2.40
2596 5300 7.779754 TTAGTACCAGTGGTGTAATTGACTA 57.220 36.000 25.64 18.20 36.19 2.59
2613 5317 9.463443 TGACTTTTCGTACTAAGTTTTAGTACC 57.537 33.333 23.27 13.50 44.14 3.34
2616 5320 8.200120 ACCTGACTTTTCGTACTAAGTTTTAGT 58.800 33.333 6.70 6.70 34.88 2.24
2628 5332 4.595762 AGCACTAACCTGACTTTTCGTA 57.404 40.909 0.00 0.00 0.00 3.43
2641 5345 2.500229 TGCCCAAGTTGTAGCACTAAC 58.500 47.619 12.43 0.00 0.00 2.34
2651 5355 4.487948 CAGTTCAATGTATGCCCAAGTTG 58.512 43.478 0.00 0.00 0.00 3.16
2653 5357 3.091545 CCAGTTCAATGTATGCCCAAGT 58.908 45.455 0.00 0.00 0.00 3.16
2676 5380 3.570559 CACGTCAAAACCAAGTTGTGTT 58.429 40.909 1.45 3.24 32.99 3.32
2677 5381 2.669950 GCACGTCAAAACCAAGTTGTGT 60.670 45.455 1.45 0.00 32.99 3.72
2700 5404 3.804688 CAAACGTGATTTGCATCGTACA 58.195 40.909 0.00 0.00 41.30 2.90
2727 5431 2.939022 GCAAGTCAGCACCGTGTC 59.061 61.111 0.00 0.00 0.00 3.67
2736 5440 4.724697 CGTTGGCGCGCAAGTCAG 62.725 66.667 34.42 14.52 41.68 3.51
2854 5559 8.598916 TGTAAACATGTCAAAGGGAGACTATAA 58.401 33.333 0.00 0.00 36.94 0.98
2855 5560 8.141298 TGTAAACATGTCAAAGGGAGACTATA 57.859 34.615 0.00 0.00 36.94 1.31
2856 5561 7.016153 TGTAAACATGTCAAAGGGAGACTAT 57.984 36.000 0.00 0.00 36.94 2.12
2864 5569 5.771469 TGCTGAATGTAAACATGTCAAAGG 58.229 37.500 0.00 0.00 36.56 3.11
2866 5571 7.710044 ACAAATGCTGAATGTAAACATGTCAAA 59.290 29.630 0.00 0.00 36.56 2.69
2872 5577 6.985117 ACTCACAAATGCTGAATGTAAACAT 58.015 32.000 0.00 0.00 38.41 2.71
2878 5583 3.755378 GGAGACTCACAAATGCTGAATGT 59.245 43.478 4.53 0.00 0.00 2.71
2912 5617 4.656575 TCCGATCAGTTATTTGGGGATACA 59.343 41.667 0.00 0.00 39.74 2.29
2938 5643 4.003614 GGCTAGGGGTTAGGCCAT 57.996 61.111 5.01 0.00 46.42 4.40
2950 5655 1.326548 GTACGCGGATTGTTTGGCTAG 59.673 52.381 12.47 0.00 0.00 3.42
2951 5656 1.337917 TGTACGCGGATTGTTTGGCTA 60.338 47.619 12.47 0.00 0.00 3.93
3017 5726 8.307582 TCTCTCGGGTCTTAAGATAAAATTCT 57.692 34.615 8.75 0.00 0.00 2.40
3021 5730 6.127168 TGCATCTCTCGGGTCTTAAGATAAAA 60.127 38.462 8.75 0.00 0.00 1.52
3036 5745 2.004733 TCAGCATTTGTGCATCTCTCG 58.995 47.619 3.03 0.00 37.25 4.04
3046 5755 8.196771 TCTGAAATTAACTTTGTCAGCATTTGT 58.803 29.630 0.00 0.00 0.00 2.83
3048 5757 9.768662 AATCTGAAATTAACTTTGTCAGCATTT 57.231 25.926 0.00 0.00 0.00 2.32
3061 5770 8.722394 AGAGAAAACGAGGAATCTGAAATTAAC 58.278 33.333 0.00 0.00 0.00 2.01
3090 5799 7.332926 GCTACGATTCACTTTATGGATCATGAT 59.667 37.037 8.25 8.25 42.95 2.45
3106 5815 5.062528 TCAATATGCCAATGCTACGATTCA 58.937 37.500 0.00 0.00 38.71 2.57
3115 5824 3.633525 TCTGTCCTTCAATATGCCAATGC 59.366 43.478 0.00 0.00 38.26 3.56
3134 5843 5.152623 TCTAGTTGATGGTGGACTTTCTG 57.847 43.478 0.00 0.00 0.00 3.02
3165 5874 1.401905 GATGGCCAAATTGACGAGGTC 59.598 52.381 10.96 0.00 0.00 3.85
3169 5878 1.543802 GGTTGATGGCCAAATTGACGA 59.456 47.619 10.96 0.00 36.36 4.20
3193 5902 3.413846 AGCTGTCATGATTGAGTGTGT 57.586 42.857 0.00 0.00 30.85 3.72
3197 5906 7.503549 TGATATGTTAGCTGTCATGATTGAGT 58.496 34.615 0.00 0.00 30.85 3.41
3232 5941 8.267183 TGACTCATTATCGCCCATGATATTTAT 58.733 33.333 0.00 0.00 31.24 1.40
3239 5948 2.224281 GGTGACTCATTATCGCCCATGA 60.224 50.000 0.00 0.00 40.30 3.07
3301 6010 5.524646 GTGTGGCCATTAAATTCAATGATGG 59.475 40.000 9.72 0.00 38.01 3.51
3328 6038 2.346803 TCATAGCTTCGTTTCTGGTGC 58.653 47.619 0.00 0.00 0.00 5.01
3330 6040 2.993899 CGTTCATAGCTTCGTTTCTGGT 59.006 45.455 0.00 0.00 0.00 4.00
3348 6058 2.569134 GAGTGGCGCTCTCTCGTT 59.431 61.111 20.43 0.00 40.98 3.85
3351 6061 2.054140 CTACCGAGTGGCGCTCTCTC 62.054 65.000 24.23 18.56 41.98 3.20
3356 6066 1.658686 CTTCTCTACCGAGTGGCGCT 61.659 60.000 7.64 0.00 39.70 5.92
3366 6076 4.495422 TCAGAATGAAACGCTTCTCTACC 58.505 43.478 0.00 0.00 45.97 3.18


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

AutoCloner maintained by Alex Coulton.