Multiple sequence alignment - TraesCS4D01G288500

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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 TraesCS4D01G288500 chr4D 100.000 2378 0 0 1 2378 459436741 459434364 0.000000e+00 4392.0
1 TraesCS4D01G288500 chr4B 90.147 1705 85 32 354 2007 574234438 574232766 0.000000e+00 2141.0
2 TraesCS4D01G288500 chr4B 96.057 279 8 1 1 276 574235124 574234846 3.600000e-123 451.0
3 TraesCS4D01G288500 chr4B 92.827 237 15 2 2004 2239 574230259 574230024 2.260000e-90 342.0
4 TraesCS4D01G288500 chr4A 90.927 1488 56 29 316 1766 9373999 9375444 0.000000e+00 1927.0
5 TraesCS4D01G288500 chr4A 94.595 222 9 1 12 233 9372586 9372804 8.140000e-90 340.0
6 TraesCS4D01G288500 chr4A 92.827 237 12 5 2004 2239 9375759 9375991 2.930000e-89 339.0
7 TraesCS4D01G288500 chr4A 94.366 213 10 1 1789 2001 9375517 9375727 2.280000e-85 326.0
8 TraesCS4D01G288500 chr4A 89.041 146 9 2 2240 2378 9376031 9376176 8.740000e-40 174.0
9 TraesCS4D01G288500 chr6A 79.070 129 20 5 107 233 149964324 149964201 5.450000e-12 82.4


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 TraesCS4D01G288500 chr4D 459434364 459436741 2377 True 4392.0 4392 100.000000 1 2378 1 chr4D.!!$R1 2377
1 TraesCS4D01G288500 chr4B 574230024 574235124 5100 True 978.0 2141 93.010333 1 2239 3 chr4B.!!$R1 2238
2 TraesCS4D01G288500 chr4A 9372586 9376176 3590 False 621.2 1927 92.351200 12 2378 5 chr4A.!!$F1 2366

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
314 1459 0.314302 ACCGTCAGTTCAGAGTTCCG 59.686 55.0 0.00 0.0 0.0 4.3 F
1018 2544 0.171007 CATGAAGCAATCGGCCGTTT 59.829 50.0 27.15 21.1 46.5 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1294 2823 0.178068 ACGATGGACACATACCTGCC 59.822 55.0 0.00 0.0 37.47 4.85 R
2308 6458 0.387202 CTCCACCGCGATCTTCATCT 59.613 55.0 8.23 0.0 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
217 221 3.628008 TCCGTATCTCTAGACCTTTGCA 58.372 45.455 0.00 0.00 0.00 4.08
288 1433 7.531280 AGATCTACTTTTGATGATTGACACG 57.469 36.000 0.00 0.00 0.00 4.49
289 1434 7.099764 AGATCTACTTTTGATGATTGACACGT 58.900 34.615 0.00 0.00 0.00 4.49
290 1435 6.706055 TCTACTTTTGATGATTGACACGTC 57.294 37.500 0.00 0.00 0.00 4.34
291 1436 4.389664 ACTTTTGATGATTGACACGTCG 57.610 40.909 0.00 0.00 0.00 5.12
292 1437 3.807622 ACTTTTGATGATTGACACGTCGT 59.192 39.130 0.00 0.00 0.00 4.34
293 1438 4.272504 ACTTTTGATGATTGACACGTCGTT 59.727 37.500 0.00 0.00 0.00 3.85
294 1439 5.464057 ACTTTTGATGATTGACACGTCGTTA 59.536 36.000 0.00 0.00 0.00 3.18
295 1440 5.908916 TTTGATGATTGACACGTCGTTAA 57.091 34.783 0.00 0.00 0.00 2.01
296 1441 4.896562 TGATGATTGACACGTCGTTAAC 57.103 40.909 0.00 0.00 0.00 2.01
297 1442 3.676172 TGATGATTGACACGTCGTTAACC 59.324 43.478 0.00 0.00 0.00 2.85
298 1443 2.052891 TGATTGACACGTCGTTAACCG 58.947 47.619 0.00 1.23 38.13 4.44
299 1444 2.053627 GATTGACACGTCGTTAACCGT 58.946 47.619 0.00 4.35 37.90 4.83
300 1445 1.476074 TTGACACGTCGTTAACCGTC 58.524 50.000 6.90 0.04 34.59 4.79
301 1446 0.380024 TGACACGTCGTTAACCGTCA 59.620 50.000 10.44 10.44 35.51 4.35
302 1447 1.047739 GACACGTCGTTAACCGTCAG 58.952 55.000 6.90 1.32 34.59 3.51
303 1448 0.381801 ACACGTCGTTAACCGTCAGT 59.618 50.000 6.90 1.86 34.59 3.41
304 1449 1.202290 ACACGTCGTTAACCGTCAGTT 60.202 47.619 6.90 0.00 42.83 3.16
305 1450 1.449418 CACGTCGTTAACCGTCAGTTC 59.551 52.381 6.90 0.00 40.05 3.01
306 1451 1.065401 ACGTCGTTAACCGTCAGTTCA 59.935 47.619 4.35 0.00 40.05 3.18
307 1452 1.712350 CGTCGTTAACCGTCAGTTCAG 59.288 52.381 0.00 0.00 40.05 3.02
308 1453 2.602933 CGTCGTTAACCGTCAGTTCAGA 60.603 50.000 0.00 0.00 40.05 3.27
309 1454 2.978489 GTCGTTAACCGTCAGTTCAGAG 59.022 50.000 0.00 0.00 40.05 3.35
310 1455 2.620115 TCGTTAACCGTCAGTTCAGAGT 59.380 45.455 0.00 0.00 40.05 3.24
311 1456 3.067180 TCGTTAACCGTCAGTTCAGAGTT 59.933 43.478 0.00 0.00 40.05 3.01
312 1457 3.424529 CGTTAACCGTCAGTTCAGAGTTC 59.575 47.826 0.00 0.00 40.05 3.01
313 1458 2.528041 AACCGTCAGTTCAGAGTTCC 57.472 50.000 0.00 0.00 30.99 3.62
314 1459 0.314302 ACCGTCAGTTCAGAGTTCCG 59.686 55.000 0.00 0.00 0.00 4.30
315 1460 0.596577 CCGTCAGTTCAGAGTTCCGA 59.403 55.000 0.00 0.00 0.00 4.55
316 1461 1.666311 CCGTCAGTTCAGAGTTCCGAC 60.666 57.143 0.00 0.00 0.00 4.79
468 1952 2.675056 GGTGCTCGCTGCTTCAGTG 61.675 63.158 0.00 1.25 42.60 3.66
539 2023 2.558359 CTCCCCTTGTAGCAAAACCAAG 59.442 50.000 0.00 0.00 36.26 3.61
687 2175 1.936547 GTGCACTGCCTAAGTAGCATC 59.063 52.381 10.32 0.00 41.63 3.91
727 2216 3.087031 CACCTGGCACTGAATTGATCTT 58.913 45.455 0.00 0.00 0.00 2.40
737 2230 8.560374 GGCACTGAATTGATCTTATAGGTTAAC 58.440 37.037 0.00 0.00 0.00 2.01
739 2232 9.613428 CACTGAATTGATCTTATAGGTTAACCA 57.387 33.333 26.26 12.70 38.89 3.67
763 2256 3.265737 TCAAGGTCCAGCTTAATGGCTAA 59.734 43.478 0.00 0.00 41.00 3.09
764 2257 3.567478 AGGTCCAGCTTAATGGCTAAG 57.433 47.619 0.00 0.00 41.00 2.18
800 2297 5.408299 TCTGGTGAATATGTGTTTTGACGAG 59.592 40.000 0.00 0.00 0.00 4.18
801 2298 4.083537 TGGTGAATATGTGTTTTGACGAGC 60.084 41.667 0.00 0.00 0.00 5.03
803 2300 3.438781 TGAATATGTGTTTTGACGAGCCC 59.561 43.478 0.00 0.00 0.00 5.19
804 2301 2.851263 TATGTGTTTTGACGAGCCCT 57.149 45.000 0.00 0.00 0.00 5.19
805 2302 2.851263 ATGTGTTTTGACGAGCCCTA 57.149 45.000 0.00 0.00 0.00 3.53
806 2303 2.163818 TGTGTTTTGACGAGCCCTAG 57.836 50.000 0.00 0.00 0.00 3.02
807 2304 0.796927 GTGTTTTGACGAGCCCTAGC 59.203 55.000 0.00 0.00 40.32 3.42
821 2318 2.465813 CCCTAGCTAGCTAGATGGCAT 58.534 52.381 40.98 12.38 46.56 4.40
822 2319 2.430332 CCCTAGCTAGCTAGATGGCATC 59.570 54.545 40.98 19.78 46.56 3.91
823 2320 3.364549 CCTAGCTAGCTAGATGGCATCT 58.635 50.000 40.98 30.89 46.56 2.90
824 2321 3.381272 CCTAGCTAGCTAGATGGCATCTC 59.619 52.174 40.98 19.22 46.56 2.75
825 2322 2.886913 AGCTAGCTAGATGGCATCTCA 58.113 47.619 31.94 17.36 40.76 3.27
826 2323 3.237746 AGCTAGCTAGATGGCATCTCAA 58.762 45.455 31.94 15.88 40.76 3.02
827 2324 3.839490 AGCTAGCTAGATGGCATCTCAAT 59.161 43.478 31.94 20.24 40.76 2.57
828 2325 4.286549 AGCTAGCTAGATGGCATCTCAATT 59.713 41.667 31.94 18.22 40.76 2.32
860 2357 8.609617 TGCAGGCTATATATAGTGAAGGTATT 57.390 34.615 18.81 0.00 32.96 1.89
877 2374 3.949113 GGTATTCCGTGCCTTTAAATCCA 59.051 43.478 0.00 0.00 0.00 3.41
879 2376 4.918810 ATTCCGTGCCTTTAAATCCATC 57.081 40.909 0.00 0.00 0.00 3.51
880 2377 3.358111 TCCGTGCCTTTAAATCCATCA 57.642 42.857 0.00 0.00 0.00 3.07
891 2388 7.414540 GCCTTTAAATCCATCACACAGAGTTAG 60.415 40.741 0.00 0.00 0.00 2.34
924 2435 5.626142 TCCAGTTAACCATTAACAAGCAGA 58.374 37.500 12.63 1.44 46.11 4.26
991 2514 3.825328 AGCTAATTACTTGGCCATCCAG 58.175 45.455 6.09 3.15 44.53 3.86
1018 2544 0.171007 CATGAAGCAATCGGCCGTTT 59.829 50.000 27.15 21.10 46.50 3.60
1128 2654 2.282674 ACGTACCAGGAGGACGCA 60.283 61.111 11.63 0.00 40.05 5.24
1182 2708 1.282248 CGGTGACCGTGTACAAGCTG 61.282 60.000 17.28 0.00 42.73 4.24
1183 2709 0.949105 GGTGACCGTGTACAAGCTGG 60.949 60.000 0.00 0.00 0.00 4.85
1196 2722 4.966787 GCTGGCCCACGGGTTCAA 62.967 66.667 0.00 0.00 37.65 2.69
1207 2733 3.555377 CCACGGGTTCAACATGTACTACA 60.555 47.826 0.00 0.00 0.00 2.74
1294 2823 2.496828 AAAGAACGGCGGGGTCTACG 62.497 60.000 13.24 0.00 0.00 3.51
1500 3050 2.095853 ACTGTTGAGTCGTTGCAGTTTG 59.904 45.455 0.00 0.00 37.12 2.93
1613 3163 1.368641 TGACGAATGGCGAATGGAAG 58.631 50.000 0.00 0.00 44.57 3.46
1619 3169 1.742761 ATGGCGAATGGAAGACACTG 58.257 50.000 0.00 0.00 0.00 3.66
1794 3394 6.367374 TGATCAGTCCTACCACATACAAAA 57.633 37.500 0.00 0.00 0.00 2.44
1795 3395 6.774673 TGATCAGTCCTACCACATACAAAAA 58.225 36.000 0.00 0.00 0.00 1.94
1943 3543 6.100004 ACAATTCTGATGTAAGTCGTCGAAT 58.900 36.000 0.00 0.00 37.15 3.34
1944 3544 6.253727 ACAATTCTGATGTAAGTCGTCGAATC 59.746 38.462 0.00 0.00 35.96 2.52
1970 3570 8.786898 CGATGATTACTGAATAATTCCAATGGT 58.213 33.333 0.00 0.00 33.37 3.55
1981 3581 9.503427 GAATAATTCCAATGGTTAGAAACTTCG 57.497 33.333 0.00 0.00 0.00 3.79
2001 3601 4.575885 TCGTTTTAAACATCTCCTGGAGG 58.424 43.478 23.00 10.83 0.00 4.30
2114 6225 7.122138 TCTGCTCTCAGTAGATCATGAATTT 57.878 36.000 0.00 0.00 41.10 1.82
2115 6226 6.985059 TCTGCTCTCAGTAGATCATGAATTTG 59.015 38.462 0.00 0.00 41.10 2.32
2116 6227 6.647229 TGCTCTCAGTAGATCATGAATTTGT 58.353 36.000 0.00 0.00 0.00 2.83
2138 6249 3.072211 CGTGTTTCCCCTTAAGTTCCTC 58.928 50.000 0.97 0.00 0.00 3.71
2151 6262 7.255139 CCCTTAAGTTCCTCAGTTGTTGTAAAG 60.255 40.741 0.97 0.00 0.00 1.85
2172 6283 3.821033 AGGACATTGTGGTTTCTGCTTAC 59.179 43.478 0.00 0.00 0.00 2.34
2189 6300 3.504520 GCTTACGGAAATTGGAAAGGACA 59.495 43.478 0.00 0.00 0.00 4.02
2200 6311 7.929941 AATTGGAAAGGACACTCTCTTTATC 57.070 36.000 0.00 0.00 33.85 1.75
2203 6314 6.231211 TGGAAAGGACACTCTCTTTATCAAC 58.769 40.000 0.00 0.00 33.85 3.18
2239 6350 6.831976 TGAATAATAAAGAGAAGAGCTCCCC 58.168 40.000 10.93 2.08 45.10 4.81
2240 6351 6.386927 TGAATAATAAAGAGAAGAGCTCCCCA 59.613 38.462 10.93 0.00 45.10 4.96
2282 6432 7.096023 CCACTGATATGAATACTAAGACAACGC 60.096 40.741 0.00 0.00 0.00 4.84
2284 6434 8.847196 ACTGATATGAATACTAAGACAACGCTA 58.153 33.333 0.00 0.00 0.00 4.26
2323 6473 1.043816 ATGGAGATGAAGATCGCGGT 58.956 50.000 6.13 0.00 33.34 5.68
2344 6494 1.728971 GGAGAAGACGCTGACATGTTG 59.271 52.381 0.00 0.00 0.00 3.33
2359 6515 8.494347 GCTGACATGTTGAACTATCATAATCTC 58.506 37.037 0.00 0.00 34.96 2.75
2374 6530 6.649155 TCATAATCTCGATGGTTTTCTTCCA 58.351 36.000 0.00 0.00 39.41 3.53
2375 6531 6.538742 TCATAATCTCGATGGTTTTCTTCCAC 59.461 38.462 0.00 0.00 37.81 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 8.621532 TCAAGGGATATGTTAGATATTGCAAC 57.378 34.615 0.00 0.00 0.00 4.17
192 196 5.764131 CAAAGGTCTAGAGATACGGATGTC 58.236 45.833 0.00 0.00 0.00 3.06
217 221 9.822727 TTTCCTCCTTAAAGAAACCAAAGATAT 57.177 29.630 0.00 0.00 0.00 1.63
291 1436 3.739810 GGAACTCTGAACTGACGGTTAAC 59.260 47.826 0.00 0.00 38.41 2.01
292 1437 3.551454 CGGAACTCTGAACTGACGGTTAA 60.551 47.826 0.00 0.00 38.41 2.01
293 1438 2.030540 CGGAACTCTGAACTGACGGTTA 60.031 50.000 0.00 0.00 38.41 2.85
294 1439 1.269621 CGGAACTCTGAACTGACGGTT 60.270 52.381 0.00 0.00 41.40 4.44
295 1440 0.314302 CGGAACTCTGAACTGACGGT 59.686 55.000 0.00 0.00 0.00 4.83
296 1441 0.596577 TCGGAACTCTGAACTGACGG 59.403 55.000 0.00 0.00 0.00 4.79
297 1442 1.666311 GGTCGGAACTCTGAACTGACG 60.666 57.143 0.00 0.00 39.80 4.35
298 1443 1.614413 AGGTCGGAACTCTGAACTGAC 59.386 52.381 5.27 0.00 46.88 3.51
299 1444 1.996798 AGGTCGGAACTCTGAACTGA 58.003 50.000 5.27 0.00 46.88 3.41
302 1447 0.733223 GCGAGGTCGGAACTCTGAAC 60.733 60.000 20.05 4.31 39.23 3.18
303 1448 1.585006 GCGAGGTCGGAACTCTGAA 59.415 57.895 20.05 0.00 40.23 3.02
304 1449 2.687805 CGCGAGGTCGGAACTCTGA 61.688 63.158 20.05 0.00 40.23 3.27
305 1450 2.202492 CGCGAGGTCGGAACTCTG 60.202 66.667 20.05 14.29 40.23 3.35
328 1473 5.685511 GTGTATTGGCGCGAATATTTTGATT 59.314 36.000 24.66 1.52 0.00 2.57
539 2023 3.047877 CCTGGTTCGCGTGGTTCC 61.048 66.667 5.77 3.50 0.00 3.62
687 2175 3.168193 GTGATTAATTGGCGTGGAAACG 58.832 45.455 0.00 0.00 0.00 3.60
727 2216 5.343715 TGGACCTTGAGTGGTTAACCTATA 58.656 41.667 24.78 2.38 41.00 1.31
737 2230 2.859165 TTAAGCTGGACCTTGAGTGG 57.141 50.000 0.00 0.00 0.00 4.00
739 2232 2.619074 GCCATTAAGCTGGACCTTGAGT 60.619 50.000 0.00 0.00 38.69 3.41
763 2256 1.614824 ACCAGAGGGCAAGCTAGCT 60.615 57.895 12.68 12.68 37.90 3.32
764 2257 1.451028 CACCAGAGGGCAAGCTAGC 60.451 63.158 6.62 6.62 37.90 3.42
765 2258 0.615331 TTCACCAGAGGGCAAGCTAG 59.385 55.000 0.00 0.00 37.90 3.42
767 2260 1.289160 TATTCACCAGAGGGCAAGCT 58.711 50.000 0.00 0.00 37.90 3.74
768 2261 1.952296 CATATTCACCAGAGGGCAAGC 59.048 52.381 0.00 0.00 37.90 4.01
770 2263 2.308570 ACACATATTCACCAGAGGGCAA 59.691 45.455 0.00 0.00 37.90 4.52
771 2264 1.915489 ACACATATTCACCAGAGGGCA 59.085 47.619 0.00 0.00 37.90 5.36
772 2265 2.717639 ACACATATTCACCAGAGGGC 57.282 50.000 0.00 0.00 37.90 5.19
774 2267 5.390885 CGTCAAAACACATATTCACCAGAGG 60.391 44.000 0.00 0.00 0.00 3.69
777 2270 5.605564 TCGTCAAAACACATATTCACCAG 57.394 39.130 0.00 0.00 0.00 4.00
800 2297 0.534873 GCCATCTAGCTAGCTAGGGC 59.465 60.000 35.99 35.99 44.45 5.19
801 2298 1.930251 TGCCATCTAGCTAGCTAGGG 58.070 55.000 38.82 33.70 44.45 3.53
803 2300 4.015764 TGAGATGCCATCTAGCTAGCTAG 58.984 47.826 36.20 36.20 45.38 3.42
804 2301 4.039603 TGAGATGCCATCTAGCTAGCTA 57.960 45.455 22.85 22.85 40.38 3.32
805 2302 2.886913 TGAGATGCCATCTAGCTAGCT 58.113 47.619 23.12 23.12 40.38 3.32
806 2303 3.674528 TTGAGATGCCATCTAGCTAGC 57.325 47.619 16.35 6.62 40.38 3.42
807 2304 6.040209 AGAATTGAGATGCCATCTAGCTAG 57.960 41.667 15.01 15.01 40.38 3.42
808 2305 5.541484 TGAGAATTGAGATGCCATCTAGCTA 59.459 40.000 7.30 0.00 40.38 3.32
809 2306 4.347292 TGAGAATTGAGATGCCATCTAGCT 59.653 41.667 7.30 0.94 40.38 3.32
810 2307 4.639334 TGAGAATTGAGATGCCATCTAGC 58.361 43.478 7.30 0.00 40.38 3.42
821 2318 1.678123 GCCTGCAGCTGAGAATTGAGA 60.678 52.381 20.43 0.00 38.99 3.27
822 2319 0.733729 GCCTGCAGCTGAGAATTGAG 59.266 55.000 20.43 0.44 38.99 3.02
823 2320 2.864114 GCCTGCAGCTGAGAATTGA 58.136 52.632 20.43 0.00 38.99 2.57
860 2357 3.013921 GTGATGGATTTAAAGGCACGGA 58.986 45.455 0.00 0.00 0.00 4.69
871 2368 5.171339 AGCTAACTCTGTGTGATGGATTT 57.829 39.130 0.00 0.00 0.00 2.17
872 2369 4.833478 AGCTAACTCTGTGTGATGGATT 57.167 40.909 0.00 0.00 0.00 3.01
877 2374 3.430098 GCAGCTAGCTAACTCTGTGTGAT 60.430 47.826 18.86 0.00 41.15 3.06
879 2376 2.266554 GCAGCTAGCTAACTCTGTGTG 58.733 52.381 18.86 2.70 41.15 3.82
880 2377 1.205893 GGCAGCTAGCTAACTCTGTGT 59.794 52.381 18.86 0.00 44.79 3.72
891 2388 1.657822 GTTAACTGGAGGCAGCTAGC 58.342 55.000 6.62 6.62 44.65 3.42
960 2483 3.760580 AGTAATTAGCTAGCTGGGCTG 57.239 47.619 27.68 0.00 40.10 4.85
991 2514 1.396440 CGATTGCTTCATGATCGTCGC 60.396 52.381 7.36 2.07 38.21 5.19
1128 2654 2.898705 CTCCTTATGAAGTCGCTGCTT 58.101 47.619 0.00 0.00 0.00 3.91
1182 2708 2.282887 ATGTTGAACCCGTGGGCC 60.283 61.111 4.41 0.00 39.32 5.80
1183 2709 0.606944 TACATGTTGAACCCGTGGGC 60.607 55.000 2.30 0.00 39.32 5.36
1192 2718 3.985279 GTGCTCGTGTAGTACATGTTGAA 59.015 43.478 19.56 8.19 40.30 2.69
1196 2722 2.257974 CGTGCTCGTGTAGTACATGT 57.742 50.000 19.56 2.69 40.58 3.21
1239 2765 1.229643 GTACTCGTAGCCCTCCCCT 59.770 63.158 0.00 0.00 0.00 4.79
1294 2823 0.178068 ACGATGGACACATACCTGCC 59.822 55.000 0.00 0.00 37.47 4.85
1405 2936 1.470632 GCATCTCTCACTCTCAACCGG 60.471 57.143 0.00 0.00 0.00 5.28
1619 3169 0.542805 TTACCCGTCCATGGTAAGCC 59.457 55.000 12.58 0.00 42.07 4.35
1656 3206 1.091771 CATCAGACGGAGCGGCAAAT 61.092 55.000 1.45 0.00 37.34 2.32
1794 3394 8.487176 GCGTTCAACAATAATCTCAACAAAATT 58.513 29.630 0.00 0.00 0.00 1.82
1795 3395 7.651304 TGCGTTCAACAATAATCTCAACAAAAT 59.349 29.630 0.00 0.00 0.00 1.82
1817 3417 3.402628 ACCTCTACTTTCATGTTGCGT 57.597 42.857 0.00 0.00 0.00 5.24
1943 3543 9.002600 CCATTGGAATTATTCAGTAATCATCGA 57.997 33.333 7.29 0.00 31.79 3.59
1944 3544 8.786898 ACCATTGGAATTATTCAGTAATCATCG 58.213 33.333 10.37 0.00 31.79 3.84
1981 3581 3.444034 GGCCTCCAGGAGATGTTTAAAAC 59.556 47.826 19.21 0.00 37.39 2.43
2001 3601 1.893919 AAAGCTGAGAGACTCCGGGC 61.894 60.000 0.00 1.11 0.00 6.13
2114 6225 3.469739 GAACTTAAGGGGAAACACGACA 58.530 45.455 7.53 0.00 40.46 4.35
2115 6226 2.810274 GGAACTTAAGGGGAAACACGAC 59.190 50.000 7.53 0.00 40.46 4.34
2116 6227 2.707257 AGGAACTTAAGGGGAAACACGA 59.293 45.455 7.53 0.00 32.80 4.35
2138 6249 5.163561 ACCACAATGTCCTTTACAACAACTG 60.164 40.000 0.00 0.00 42.70 3.16
2151 6262 3.364964 CGTAAGCAGAAACCACAATGTCC 60.365 47.826 0.00 0.00 0.00 4.02
2172 6283 3.412386 AGAGTGTCCTTTCCAATTTCCG 58.588 45.455 0.00 0.00 0.00 4.30
2189 6300 9.566432 AGTCATCTTTTTGTTGATAAAGAGAGT 57.434 29.630 0.00 0.00 41.96 3.24
2239 6350 1.588674 TGGTAACCACTGAAAGCGTG 58.411 50.000 0.00 0.00 37.60 5.34
2308 6458 0.387202 CTCCACCGCGATCTTCATCT 59.613 55.000 8.23 0.00 0.00 2.90
2317 6467 4.415332 GCGTCTTCTCCACCGCGA 62.415 66.667 8.23 0.00 36.53 5.87
2323 6473 0.969149 ACATGTCAGCGTCTTCTCCA 59.031 50.000 0.00 0.00 0.00 3.86
2344 6494 9.482627 AGAAAACCATCGAGATTATGATAGTTC 57.517 33.333 0.00 0.00 28.49 3.01


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

AutoCloner maintained by Alex Coulton.