Multiple sequence alignment - TraesCS3A01G176000

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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 TraesCS3A01G176000 chr3A 100.000 2405 0 0 1 2405 196421632 196419228 0.000000e+00 4442
1 TraesCS3A01G176000 chr3A 92.157 102 8 0 2304 2405 750652600 750652499 6.930000e-31 145
2 TraesCS3A01G176000 chr3D 91.543 2365 97 36 1 2321 164401411 164399106 0.000000e+00 3164
3 TraesCS3A01G176000 chr3B 89.878 2371 108 46 1 2321 240409162 240406874 0.000000e+00 2928
4 TraesCS3A01G176000 chr1A 96.591 88 3 0 2318 2405 509646894 509646807 1.930000e-31 147
5 TraesCS3A01G176000 chr4B 93.750 96 6 0 2310 2405 591495274 591495369 6.930000e-31 145
6 TraesCS3A01G176000 chr5A 93.617 94 6 0 2312 2405 540272117 540272024 8.960000e-30 141
7 TraesCS3A01G176000 chr5A 95.349 86 4 0 2320 2405 658367078 658366993 1.160000e-28 137
8 TraesCS3A01G176000 chr4D 93.617 94 6 0 2312 2405 131716372 131716465 8.960000e-30 141
9 TraesCS3A01G176000 chr7D 92.784 97 5 2 2310 2405 32052861 32052766 3.220000e-29 139
10 TraesCS3A01G176000 chr1D 92.000 100 7 1 2307 2405 422402512 422402611 3.220000e-29 139
11 TraesCS3A01G176000 chr6B 95.349 86 4 0 2320 2405 409459494 409459409 1.160000e-28 137


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 TraesCS3A01G176000 chr3A 196419228 196421632 2404 True 4442 4442 100.000 1 2405 1 chr3A.!!$R1 2404
1 TraesCS3A01G176000 chr3D 164399106 164401411 2305 True 3164 3164 91.543 1 2321 1 chr3D.!!$R1 2320
2 TraesCS3A01G176000 chr3B 240406874 240409162 2288 True 2928 2928 89.878 1 2321 1 chr3B.!!$R1 2320

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
832 858 0.106469 CATCTCTCCCTCGTCTCCCA 60.106 60.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1902 0.178995 TGGCATGTCAGGCTCACAAA 60.179 50.0 9.66 0.0 34.73 2.83 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
79 91 2.297701 GTTGACCTGGAACACACACAT 58.702 47.619 0.00 0.00 0.00 3.21
80 92 3.118223 TGTTGACCTGGAACACACACATA 60.118 43.478 0.00 0.00 0.00 2.29
122 134 7.010339 AGTGGCTTAGATATAGGACCATTTC 57.990 40.000 0.00 0.00 0.00 2.17
123 135 6.558775 AGTGGCTTAGATATAGGACCATTTCA 59.441 38.462 0.00 0.00 0.00 2.69
215 235 4.261072 CGTACGTCCATAGAGTATGTTGCT 60.261 45.833 7.22 0.00 34.36 3.91
216 236 5.049886 CGTACGTCCATAGAGTATGTTGCTA 60.050 44.000 7.22 0.00 34.36 3.49
217 237 5.184340 ACGTCCATAGAGTATGTTGCTAC 57.816 43.478 0.00 0.00 34.36 3.58
218 238 4.888239 ACGTCCATAGAGTATGTTGCTACT 59.112 41.667 0.00 0.00 34.65 2.57
219 239 5.008811 ACGTCCATAGAGTATGTTGCTACTC 59.991 44.000 0.00 1.40 45.26 2.59
220 240 5.563085 CGTCCATAGAGTATGTTGCTACTCC 60.563 48.000 7.12 0.00 45.80 3.85
221 241 5.302059 GTCCATAGAGTATGTTGCTACTCCA 59.698 44.000 7.12 0.00 45.80 3.86
222 242 6.015010 GTCCATAGAGTATGTTGCTACTCCAT 60.015 42.308 7.12 0.00 45.80 3.41
223 243 6.015095 TCCATAGAGTATGTTGCTACTCCATG 60.015 42.308 10.39 10.39 45.80 3.66
224 244 6.239430 CCATAGAGTATGTTGCTACTCCATGT 60.239 42.308 13.99 0.00 45.80 3.21
292 312 3.820425 GTCCATCTGACACCCCCA 58.180 61.111 0.00 0.00 43.85 4.96
293 313 2.311287 GTCCATCTGACACCCCCAT 58.689 57.895 0.00 0.00 43.85 4.00
294 314 0.181350 GTCCATCTGACACCCCCATC 59.819 60.000 0.00 0.00 43.85 3.51
299 319 1.125093 TCTGACACCCCCATCACGTT 61.125 55.000 0.00 0.00 0.00 3.99
301 321 1.002659 CTGACACCCCCATCACGTTTA 59.997 52.381 0.00 0.00 0.00 2.01
327 347 1.463444 GATGTGCCCAAGTTGTACGAC 59.537 52.381 4.97 4.97 0.00 4.34
400 420 3.858247 AGTAAATACAGCCGAACACTCC 58.142 45.455 0.00 0.00 0.00 3.85
411 431 2.224079 CCGAACACTCCAAATGACACTG 59.776 50.000 0.00 0.00 0.00 3.66
446 466 1.218875 TAGTGACGGTTTGCAGCACG 61.219 55.000 0.00 0.00 34.82 5.34
573 594 8.298729 ACTCCAATTCTTCTTTTTCAGTTTCT 57.701 30.769 0.00 0.00 0.00 2.52
574 595 8.753133 ACTCCAATTCTTCTTTTTCAGTTTCTT 58.247 29.630 0.00 0.00 0.00 2.52
575 596 9.591792 CTCCAATTCTTCTTTTTCAGTTTCTTT 57.408 29.630 0.00 0.00 0.00 2.52
602 623 1.228245 CACCTGGTCCAACACCCAG 60.228 63.158 0.00 0.00 46.18 4.45
604 625 2.282462 CTGGTCCAACACCCAGGC 60.282 66.667 0.00 0.00 46.18 4.85
605 626 3.868200 CTGGTCCAACACCCAGGCC 62.868 68.421 0.00 0.00 46.18 5.19
606 627 3.897122 GGTCCAACACCCAGGCCA 61.897 66.667 5.01 0.00 39.69 5.36
607 628 2.197324 GTCCAACACCCAGGCCAA 59.803 61.111 5.01 0.00 0.00 4.52
608 629 1.903404 GTCCAACACCCAGGCCAAG 60.903 63.158 5.01 0.00 0.00 3.61
609 630 2.081787 TCCAACACCCAGGCCAAGA 61.082 57.895 5.01 0.00 0.00 3.02
610 631 1.077265 CCAACACCCAGGCCAAGAT 59.923 57.895 5.01 0.00 0.00 2.40
612 633 0.540365 CAACACCCAGGCCAAGATGT 60.540 55.000 5.01 0.39 0.00 3.06
613 634 1.072266 AACACCCAGGCCAAGATGTA 58.928 50.000 5.01 0.00 0.00 2.29
617 638 0.250467 CCCAGGCCAAGATGTATCGG 60.250 60.000 5.01 0.00 0.00 4.18
825 851 4.637489 CGCGCCATCTCTCCCTCG 62.637 72.222 0.00 0.00 0.00 4.63
826 852 3.532155 GCGCCATCTCTCCCTCGT 61.532 66.667 0.00 0.00 0.00 4.18
827 853 2.725008 CGCCATCTCTCCCTCGTC 59.275 66.667 0.00 0.00 0.00 4.20
828 854 1.826054 CGCCATCTCTCCCTCGTCT 60.826 63.158 0.00 0.00 0.00 4.18
832 858 0.106469 CATCTCTCCCTCGTCTCCCA 60.106 60.000 0.00 0.00 0.00 4.37
913 959 3.936203 GAGTCCCACACACGCCCA 61.936 66.667 0.00 0.00 0.00 5.36
1347 1394 2.925706 TACAACTGCCAGCCCGGA 60.926 61.111 0.73 0.00 36.56 5.14
1406 1453 2.124403 CCAGTGCAGGGGCTGATC 60.124 66.667 3.73 0.00 41.91 2.92
1441 1491 3.308402 CCCTGCTTCATTCCTTCTTACCA 60.308 47.826 0.00 0.00 0.00 3.25
1442 1492 3.691609 CCTGCTTCATTCCTTCTTACCAC 59.308 47.826 0.00 0.00 0.00 4.16
1443 1493 3.686016 TGCTTCATTCCTTCTTACCACC 58.314 45.455 0.00 0.00 0.00 4.61
1465 1515 5.008331 CCTGCATGCCTCATCAATTAGTAT 58.992 41.667 16.68 0.00 0.00 2.12
1555 1605 3.959293 TGCTTGATCAATCATCACTGGT 58.041 40.909 8.96 0.00 41.56 4.00
1556 1606 3.692593 TGCTTGATCAATCATCACTGGTG 59.307 43.478 8.96 0.00 41.56 4.17
1559 1609 2.092267 TGATCAATCATCACTGGTGGGG 60.092 50.000 0.00 0.00 36.51 4.96
1568 1618 4.284550 CTGGTGGGGGTGGTGTGG 62.285 72.222 0.00 0.00 0.00 4.17
1601 1653 2.818132 GGATCACTGGAGGAGGCG 59.182 66.667 0.00 0.00 0.00 5.52
1613 1665 3.181458 TGGAGGAGGCGTGGTTAATTATC 60.181 47.826 0.00 0.00 0.00 1.75
1657 1709 5.253335 GGTGAAAGTAATTAAGCTTACGCG 58.747 41.667 5.45 3.53 42.32 6.01
1660 1712 6.460763 GTGAAAGTAATTAAGCTTACGCGTTC 59.539 38.462 20.78 7.47 42.32 3.95
1661 1713 6.366877 TGAAAGTAATTAAGCTTACGCGTTCT 59.633 34.615 20.78 9.99 42.32 3.01
1662 1714 5.697848 AGTAATTAAGCTTACGCGTTCTG 57.302 39.130 20.78 9.38 42.32 3.02
1663 1715 4.565564 AGTAATTAAGCTTACGCGTTCTGG 59.434 41.667 20.78 6.57 42.32 3.86
1664 1716 2.443887 TTAAGCTTACGCGTTCTGGT 57.556 45.000 20.78 10.98 42.32 4.00
1665 1717 1.705256 TAAGCTTACGCGTTCTGGTG 58.295 50.000 20.78 2.69 42.32 4.17
1701 1753 5.867174 GGTTGTGCCCAATAAATTTGTAGAC 59.133 40.000 0.00 0.00 32.11 2.59
1795 1857 0.330604 ATGTGCTTCTCTGCCATGGT 59.669 50.000 14.67 0.00 0.00 3.55
1836 1901 3.027419 GCAGGTGGCAGAGAAGTTT 57.973 52.632 0.00 0.00 43.97 2.66
1837 1902 1.322442 GCAGGTGGCAGAGAAGTTTT 58.678 50.000 0.00 0.00 43.97 2.43
1838 1903 1.683385 GCAGGTGGCAGAGAAGTTTTT 59.317 47.619 0.00 0.00 43.97 1.94
1944 2009 8.926092 ATATATTTACCTTTCTCCTTTCTGCC 57.074 34.615 0.00 0.00 0.00 4.85
1963 2028 1.708551 CCCCCTCCTTGTTTCTGGTTA 59.291 52.381 0.00 0.00 0.00 2.85
1970 2035 3.826157 TCCTTGTTTCTGGTTAGCCAATG 59.174 43.478 0.00 0.00 45.51 2.82
2123 2196 6.768381 GTGGAGCTTCTTTGGCTATACTTAAT 59.232 38.462 0.00 0.00 40.40 1.40
2161 2234 7.589954 ACACTTTAACACGATTCATTTGTTAGC 59.410 33.333 0.00 0.00 37.11 3.09
2180 2253 1.340889 GCACCAACACACAATGTCCAT 59.659 47.619 0.00 0.00 42.31 3.41
2209 2282 2.131183 GCTGTCACGCTTCATCCTATC 58.869 52.381 0.00 0.00 0.00 2.08
2301 2374 4.071961 TCTAGAAGTGCACAAGCTCAAA 57.928 40.909 21.04 2.13 42.74 2.69
2337 2410 6.915349 AGATATACTAGAAGAACATCCGTGC 58.085 40.000 0.00 0.00 0.00 5.34
2338 2411 2.279582 ACTAGAAGAACATCCGTGCG 57.720 50.000 0.00 0.00 0.00 5.34
2339 2412 1.544691 ACTAGAAGAACATCCGTGCGT 59.455 47.619 0.00 0.00 0.00 5.24
2340 2413 2.029290 ACTAGAAGAACATCCGTGCGTT 60.029 45.455 0.00 0.00 0.00 4.84
2341 2414 1.148310 AGAAGAACATCCGTGCGTTG 58.852 50.000 0.00 0.00 0.00 4.10
2342 2415 0.452784 GAAGAACATCCGTGCGTTGC 60.453 55.000 0.00 0.00 0.00 4.17
2343 2416 1.163420 AAGAACATCCGTGCGTTGCA 61.163 50.000 0.00 0.00 35.60 4.08
2344 2417 1.163420 AGAACATCCGTGCGTTGCAA 61.163 50.000 0.00 0.00 41.47 4.08
2345 2418 0.996727 GAACATCCGTGCGTTGCAAC 60.997 55.000 19.89 19.89 41.47 4.17
2355 2428 3.354678 GTTGCAACGAGGCCACAT 58.645 55.556 14.90 0.00 30.39 3.21
2356 2429 1.659794 GTTGCAACGAGGCCACATT 59.340 52.632 14.90 0.00 30.39 2.71
2357 2430 0.878416 GTTGCAACGAGGCCACATTA 59.122 50.000 14.90 0.00 30.39 1.90
2358 2431 1.268352 GTTGCAACGAGGCCACATTAA 59.732 47.619 14.90 0.00 30.39 1.40
2359 2432 0.878416 TGCAACGAGGCCACATTAAC 59.122 50.000 5.01 0.00 0.00 2.01
2360 2433 1.165270 GCAACGAGGCCACATTAACT 58.835 50.000 5.01 0.00 0.00 2.24
2361 2434 1.539827 GCAACGAGGCCACATTAACTT 59.460 47.619 5.01 0.00 0.00 2.66
2362 2435 2.030274 GCAACGAGGCCACATTAACTTT 60.030 45.455 5.01 0.00 0.00 2.66
2363 2436 3.189702 GCAACGAGGCCACATTAACTTTA 59.810 43.478 5.01 0.00 0.00 1.85
2364 2437 4.320641 GCAACGAGGCCACATTAACTTTAA 60.321 41.667 5.01 0.00 0.00 1.52
2365 2438 5.390613 CAACGAGGCCACATTAACTTTAAG 58.609 41.667 5.01 0.00 0.00 1.85
2366 2439 4.901868 ACGAGGCCACATTAACTTTAAGA 58.098 39.130 5.01 0.00 0.00 2.10
2367 2440 4.935808 ACGAGGCCACATTAACTTTAAGAG 59.064 41.667 5.01 0.00 0.00 2.85
2368 2441 4.935808 CGAGGCCACATTAACTTTAAGAGT 59.064 41.667 5.01 0.00 41.47 3.24
2370 2443 6.402226 CGAGGCCACATTAACTTTAAGAGTTC 60.402 42.308 5.01 0.00 45.40 3.01
2371 2444 6.303839 AGGCCACATTAACTTTAAGAGTTCA 58.696 36.000 5.01 0.00 45.40 3.18
2372 2445 6.775629 AGGCCACATTAACTTTAAGAGTTCAA 59.224 34.615 5.01 2.81 45.40 2.69
2373 2446 7.451566 AGGCCACATTAACTTTAAGAGTTCAAT 59.548 33.333 5.01 4.32 45.40 2.57
2374 2447 8.736244 GGCCACATTAACTTTAAGAGTTCAATA 58.264 33.333 0.00 0.00 45.40 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 91 5.672503 CCACTAGACTAGCACTAGACAGTA 58.327 45.833 22.85 0.00 39.48 2.74
80 92 4.519213 CCACTAGACTAGCACTAGACAGT 58.481 47.826 22.85 7.88 39.48 3.55
122 134 2.543430 CTGTCCCCGCAAAACAAAAATG 59.457 45.455 0.00 0.00 0.00 2.32
123 135 2.484594 CCTGTCCCCGCAAAACAAAAAT 60.485 45.455 0.00 0.00 0.00 1.82
129 149 2.265904 GGTCCTGTCCCCGCAAAAC 61.266 63.158 0.00 0.00 0.00 2.43
199 219 6.352016 ATGGAGTAGCAACATACTCTATGG 57.648 41.667 10.72 0.00 46.30 2.74
215 235 4.104086 ACTCCTTTCATGGACATGGAGTA 58.896 43.478 16.70 2.55 35.96 2.59
216 236 2.915604 ACTCCTTTCATGGACATGGAGT 59.084 45.455 13.85 13.85 39.24 3.85
217 237 3.641434 ACTCCTTTCATGGACATGGAG 57.359 47.619 11.98 12.84 39.24 3.86
218 238 3.118261 GCTACTCCTTTCATGGACATGGA 60.118 47.826 11.98 0.49 39.24 3.41
219 239 3.209410 GCTACTCCTTTCATGGACATGG 58.791 50.000 11.98 0.00 39.24 3.66
220 240 3.624861 GTGCTACTCCTTTCATGGACATG 59.375 47.826 5.95 5.95 40.09 3.21
221 241 3.521126 AGTGCTACTCCTTTCATGGACAT 59.479 43.478 0.00 0.00 31.94 3.06
222 242 2.906389 AGTGCTACTCCTTTCATGGACA 59.094 45.455 0.00 0.00 31.94 4.02
223 243 3.055819 TCAGTGCTACTCCTTTCATGGAC 60.056 47.826 0.00 0.00 31.94 4.02
224 244 3.173151 TCAGTGCTACTCCTTTCATGGA 58.827 45.455 0.00 0.00 34.52 3.41
292 312 5.592282 TGGGCACATCAATAATAAACGTGAT 59.408 36.000 0.00 0.00 0.00 3.06
293 313 4.944317 TGGGCACATCAATAATAAACGTGA 59.056 37.500 0.00 0.00 0.00 4.35
294 314 5.242069 TGGGCACATCAATAATAAACGTG 57.758 39.130 0.00 0.00 0.00 4.49
299 319 6.849085 ACAACTTGGGCACATCAATAATAA 57.151 33.333 0.00 0.00 0.00 1.40
301 321 5.163663 CGTACAACTTGGGCACATCAATAAT 60.164 40.000 0.00 0.00 0.00 1.28
327 347 1.787155 GTAGATATGAACAGCGCACCG 59.213 52.381 11.47 0.00 0.00 4.94
359 379 1.009222 GTGCGCATCAATGGCTAGC 60.009 57.895 15.91 6.04 0.00 3.42
400 420 6.551385 AGCTTACTTTCTCAGTGTCATTTG 57.449 37.500 0.00 0.00 35.97 2.32
411 431 5.267776 CGTCACTAGCTAGCTTACTTTCTC 58.732 45.833 24.88 5.76 0.00 2.87
446 466 3.726291 TTTACTTGCACCTGCTTTTCC 57.274 42.857 0.00 0.00 42.66 3.13
489 509 1.745653 GTTGCTACATCTTTGGGAGGC 59.254 52.381 0.00 0.00 0.00 4.70
571 592 2.203938 AGGTGCCCGGGAGAAAGA 60.204 61.111 29.31 0.00 0.00 2.52
572 593 2.045926 CAGGTGCCCGGGAGAAAG 60.046 66.667 29.31 6.46 0.00 2.62
573 594 3.646715 CCAGGTGCCCGGGAGAAA 61.647 66.667 29.31 2.38 41.43 2.52
574 595 4.974438 ACCAGGTGCCCGGGAGAA 62.974 66.667 29.31 5.59 41.43 2.87
604 625 1.338337 AGACGAGCCGATACATCTTGG 59.662 52.381 1.50 0.00 0.00 3.61
605 626 2.656085 GAGACGAGCCGATACATCTTG 58.344 52.381 1.50 0.00 0.00 3.02
606 627 1.264557 CGAGACGAGCCGATACATCTT 59.735 52.381 1.50 0.00 0.00 2.40
607 628 0.869068 CGAGACGAGCCGATACATCT 59.131 55.000 1.50 0.00 0.00 2.90
608 629 0.587285 ACGAGACGAGCCGATACATC 59.413 55.000 1.50 0.00 0.00 3.06
609 630 0.308068 CACGAGACGAGCCGATACAT 59.692 55.000 1.50 0.00 0.00 2.29
610 631 0.741927 TCACGAGACGAGCCGATACA 60.742 55.000 1.50 0.00 0.00 2.29
612 633 0.866427 GATCACGAGACGAGCCGATA 59.134 55.000 1.50 0.00 0.00 2.92
613 634 1.649815 GATCACGAGACGAGCCGAT 59.350 57.895 1.50 0.00 0.00 4.18
617 638 1.203928 CATTGGATCACGAGACGAGC 58.796 55.000 0.00 0.00 0.00 5.03
649 670 2.544267 GGATTGGATGGTTCGATTCGTC 59.456 50.000 5.89 1.15 0.00 4.20
825 851 5.175127 GTGAGAAGAGAAAGAATGGGAGAC 58.825 45.833 0.00 0.00 0.00 3.36
826 852 4.223923 GGTGAGAAGAGAAAGAATGGGAGA 59.776 45.833 0.00 0.00 0.00 3.71
827 853 4.224818 AGGTGAGAAGAGAAAGAATGGGAG 59.775 45.833 0.00 0.00 0.00 4.30
828 854 4.171234 AGGTGAGAAGAGAAAGAATGGGA 58.829 43.478 0.00 0.00 0.00 4.37
832 858 5.623368 CGCAGTAGGTGAGAAGAGAAAGAAT 60.623 44.000 0.00 0.00 0.00 2.40
913 959 1.672356 GGCGATGTGTGGAGCTGTT 60.672 57.895 0.00 0.00 0.00 3.16
945 991 2.010582 GCTAGCTGTGGACGGAGGAG 62.011 65.000 7.70 0.00 0.00 3.69
1320 1367 0.902531 GGCAGTTGTAGTAGGAGGCA 59.097 55.000 0.00 0.00 0.00 4.75
1347 1394 4.733725 TAGGGGTTGGCCTCGGCT 62.734 66.667 3.32 0.00 41.22 5.52
1406 1453 2.532250 AGCAGGGTTTAATGAAGGGG 57.468 50.000 0.00 0.00 0.00 4.79
1408 1455 5.394553 GGAATGAAGCAGGGTTTAATGAAGG 60.395 44.000 0.00 0.00 0.00 3.46
1441 1491 2.154567 AATTGATGAGGCATGCAGGT 57.845 45.000 21.36 2.61 0.00 4.00
1442 1492 3.220110 ACTAATTGATGAGGCATGCAGG 58.780 45.455 21.36 0.00 0.00 4.85
1443 1493 6.379386 CAATACTAATTGATGAGGCATGCAG 58.621 40.000 21.36 6.41 44.50 4.41
1555 1605 2.075355 GATTGACCACACCACCCCCA 62.075 60.000 0.00 0.00 0.00 4.96
1556 1606 1.304134 GATTGACCACACCACCCCC 60.304 63.158 0.00 0.00 0.00 5.40
1559 1609 1.435577 GTACGATTGACCACACCACC 58.564 55.000 0.00 0.00 0.00 4.61
1585 1635 1.142748 CACGCCTCCTCCAGTGATC 59.857 63.158 0.00 0.00 36.79 2.92
1601 1653 6.250527 GCACAAATGACACGATAATTAACCAC 59.749 38.462 0.00 0.00 0.00 4.16
1613 1665 3.500982 CCAAATAGGCACAAATGACACG 58.499 45.455 0.00 0.00 35.60 4.49
1657 1709 2.096496 CCGAAATCAGATGCACCAGAAC 59.904 50.000 0.00 0.00 0.00 3.01
1660 1712 1.742761 ACCGAAATCAGATGCACCAG 58.257 50.000 0.00 0.00 0.00 4.00
1661 1713 1.811965 CAACCGAAATCAGATGCACCA 59.188 47.619 0.00 0.00 0.00 4.17
1662 1714 1.812571 ACAACCGAAATCAGATGCACC 59.187 47.619 0.00 0.00 0.00 5.01
1663 1715 2.855180 CACAACCGAAATCAGATGCAC 58.145 47.619 0.00 0.00 0.00 4.57
1664 1716 1.199789 GCACAACCGAAATCAGATGCA 59.800 47.619 0.00 0.00 0.00 3.96
1665 1717 1.468054 GGCACAACCGAAATCAGATGC 60.468 52.381 0.00 0.00 0.00 3.91
1701 1753 4.492611 GAAGGAAGTACGTACCAAAGGAG 58.507 47.826 21.80 0.00 0.00 3.69
1795 1857 7.499292 TGCTCAATCAAGAAAATGGAGAAAAA 58.501 30.769 0.00 0.00 0.00 1.94
1836 1901 0.961019 GGCATGTCAGGCTCACAAAA 59.039 50.000 9.66 0.00 0.00 2.44
1837 1902 0.178995 TGGCATGTCAGGCTCACAAA 60.179 50.000 9.66 0.00 34.73 2.83
1838 1903 0.178995 TTGGCATGTCAGGCTCACAA 60.179 50.000 9.66 2.60 34.73 3.33
1944 2009 2.880167 GCTAACCAGAAACAAGGAGGGG 60.880 54.545 0.00 0.00 0.00 4.79
1963 2028 4.157289 CAGAGCACTGATTAAACATTGGCT 59.843 41.667 5.03 5.67 46.03 4.75
2123 2196 8.659925 TCGTGTTAAAGTGTACAAGGAATAAA 57.340 30.769 0.00 0.00 0.00 1.40
2144 2217 4.418013 TGGTGCTAACAAATGAATCGTG 57.582 40.909 0.00 0.00 0.00 4.35
2161 2234 2.361757 ACATGGACATTGTGTGTTGGTG 59.638 45.455 0.00 0.00 42.36 4.17
2180 2253 2.203139 CGTGACAGCCCAACCACA 60.203 61.111 0.00 0.00 0.00 4.17
2250 2323 3.065371 GCGAATGTAAGATTCCACAAGGG 59.935 47.826 0.00 0.00 34.83 3.95
2321 2394 2.333926 CAACGCACGGATGTTCTTCTA 58.666 47.619 0.00 0.00 0.00 2.10
2322 2395 1.148310 CAACGCACGGATGTTCTTCT 58.852 50.000 0.00 0.00 0.00 2.85
2323 2396 0.452784 GCAACGCACGGATGTTCTTC 60.453 55.000 0.00 0.00 0.00 2.87
2324 2397 1.163420 TGCAACGCACGGATGTTCTT 61.163 50.000 0.00 0.00 31.71 2.52
2325 2398 1.163420 TTGCAACGCACGGATGTTCT 61.163 50.000 0.00 0.00 38.71 3.01
2326 2399 0.996727 GTTGCAACGCACGGATGTTC 60.997 55.000 14.90 0.00 38.71 3.18
2327 2400 1.008995 GTTGCAACGCACGGATGTT 60.009 52.632 14.90 0.00 38.71 2.71
2328 2401 2.637025 GTTGCAACGCACGGATGT 59.363 55.556 14.90 0.00 38.71 3.06
2329 2402 2.499520 CGTTGCAACGCACGGATG 60.500 61.111 35.89 10.57 46.06 3.51
2338 2411 0.878416 TAATGTGGCCTCGTTGCAAC 59.122 50.000 19.89 19.89 35.65 4.17
2339 2412 1.268352 GTTAATGTGGCCTCGTTGCAA 59.732 47.619 20.11 6.68 0.00 4.08
2340 2413 0.878416 GTTAATGTGGCCTCGTTGCA 59.122 50.000 20.11 6.05 0.00 4.08
2341 2414 1.165270 AGTTAATGTGGCCTCGTTGC 58.835 50.000 20.11 13.21 0.00 4.17
2342 2415 3.915437 AAAGTTAATGTGGCCTCGTTG 57.085 42.857 20.11 0.00 0.00 4.10
2343 2416 5.310451 TCTTAAAGTTAATGTGGCCTCGTT 58.690 37.500 16.09 16.09 0.00 3.85
2344 2417 4.901868 TCTTAAAGTTAATGTGGCCTCGT 58.098 39.130 3.32 0.00 0.00 4.18
2345 2418 4.935808 ACTCTTAAAGTTAATGTGGCCTCG 59.064 41.667 3.32 0.00 33.03 4.63
2346 2419 6.819397 AACTCTTAAAGTTAATGTGGCCTC 57.181 37.500 3.32 0.00 46.55 4.70


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

AutoCloner maintained by Alex Coulton.