Multiple sequence alignment - TraesCS5D01G159600

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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 TraesCS5D01G159600 chr5D 100.000 3359 0 0 1 3359 249256270 249259628 0.000000e+00 6204.0
1 TraesCS5D01G159600 chr5B 94.338 2985 98 28 391 3359 282044637 282047566 0.000000e+00 4510.0
2 TraesCS5D01G159600 chr5B 87.023 131 14 3 594 721 288327672 288327802 9.710000e-31 145.0
3 TraesCS5D01G159600 chr5A 96.405 918 30 2 1810 2726 331943560 331944475 0.000000e+00 1509.0
4 TraesCS5D01G159600 chr5A 91.012 1057 68 12 393 1434 331940643 331941687 0.000000e+00 1400.0
5 TraesCS5D01G159600 chr5A 94.800 500 23 3 2862 3359 331944470 331944968 0.000000e+00 776.0
6 TraesCS5D01G159600 chr5A 87.946 224 18 3 1 222 331940425 331940641 4.300000e-64 255.0
7 TraesCS5D01G159600 chrUn 100.000 427 0 0 1961 2387 476491497 476491923 0.000000e+00 789.0
8 TraesCS5D01G159600 chr1A 92.899 169 9 1 1644 1812 388749794 388749959 3.350000e-60 243.0
9 TraesCS5D01G159600 chr1A 91.617 167 13 1 1644 1810 7230254 7230089 2.610000e-56 230.0
10 TraesCS5D01G159600 chr2D 91.566 166 13 1 1643 1808 82141327 82141163 9.380000e-56 228.0
11 TraesCS5D01G159600 chr2D 88.618 123 13 1 594 715 512769208 512769330 7.510000e-32 148.0
12 TraesCS5D01G159600 chr3B 90.588 170 15 1 1643 1811 107966271 107966102 1.210000e-54 224.0
13 TraesCS5D01G159600 chr3B 89.286 56 3 3 451 505 818868256 818868309 2.160000e-07 67.6
14 TraesCS5D01G159600 chr6D 89.412 170 16 1 1643 1812 208769721 208769888 2.630000e-51 213.0
15 TraesCS5D01G159600 chr6D 88.824 170 17 1 1643 1812 208743726 208743893 1.220000e-49 207.0
16 TraesCS5D01G159600 chr2B 89.820 167 15 1 1648 1812 85072240 85072406 2.630000e-51 213.0
17 TraesCS5D01G159600 chr2B 88.304 171 18 2 1643 1812 765556389 765556220 1.580000e-48 204.0
18 TraesCS5D01G159600 chr2B 88.710 124 12 2 594 715 602996316 602996439 2.090000e-32 150.0
19 TraesCS5D01G159600 chr1D 89.286 168 16 2 1643 1809 330094176 330094342 3.400000e-50 209.0
20 TraesCS5D01G159600 chr1D 90.551 127 9 2 592 717 79358260 79358136 7.460000e-37 165.0
21 TraesCS5D01G159600 chr1B 92.000 125 9 1 594 717 130540304 130540180 1.240000e-39 174.0
22 TraesCS5D01G159600 chr6B 90.083 121 10 2 594 713 233039360 233039241 4.490000e-34 156.0
23 TraesCS5D01G159600 chr7A 85.517 145 13 7 597 734 427814985 427814842 9.710000e-31 145.0


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 TraesCS5D01G159600 chr5D 249256270 249259628 3358 False 6204 6204 100.00000 1 3359 1 chr5D.!!$F1 3358
1 TraesCS5D01G159600 chr5B 282044637 282047566 2929 False 4510 4510 94.33800 391 3359 1 chr5B.!!$F1 2968
2 TraesCS5D01G159600 chr5A 331940425 331944968 4543 False 985 1509 92.54075 1 3359 4 chr5A.!!$F1 3358

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
304 307 0.036732 TGGGATGTTGACCACTGCTC 59.963 55.0 0.00 0.00 0.0 4.26 F
306 309 0.036732 GGATGTTGACCACTGCTCCA 59.963 55.0 0.00 0.00 0.0 3.86 F
329 332 0.259065 TATGGGCCGGGCAAAATACA 59.741 50.0 30.95 17.47 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1533 1587 1.479323 TGTATAGCAAGACCGTGGGAC 59.521 52.381 0.0 0.0 0.00 4.46 R
1947 3658 2.203294 GCAACGTTCCCTGGTGGT 60.203 61.111 0.0 0.0 34.77 4.16 R
2508 4219 3.377172 ACCAGCAAGTTTCACAGTACAAC 59.623 43.478 0.0 0.0 0.00 3.32 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
52 53 6.765512 TGATTTATGATGGTGCGTCAAATAGA 59.234 34.615 0.00 0.00 32.88 1.98
94 96 0.978146 AGTCAGGATTGGGACCTCCG 60.978 60.000 0.00 0.00 38.76 4.63
108 110 3.792053 CTCCGATTCCCCGCCTTCG 62.792 68.421 0.00 0.00 0.00 3.79
144 146 1.014044 ATAACAGGCACACACGCTCG 61.014 55.000 0.00 0.00 0.00 5.03
167 169 4.759782 CTCTACACCCTTTGACCACTATG 58.240 47.826 0.00 0.00 0.00 2.23
172 174 5.697067 ACACCCTTTGACCACTATGTTTTA 58.303 37.500 0.00 0.00 0.00 1.52
173 175 5.768164 ACACCCTTTGACCACTATGTTTTAG 59.232 40.000 0.00 0.00 0.00 1.85
174 176 4.765339 ACCCTTTGACCACTATGTTTTAGC 59.235 41.667 0.00 0.00 0.00 3.09
175 177 4.764823 CCCTTTGACCACTATGTTTTAGCA 59.235 41.667 0.00 0.00 0.00 3.49
176 178 5.418840 CCCTTTGACCACTATGTTTTAGCAT 59.581 40.000 0.00 0.00 0.00 3.79
177 179 6.324819 CCTTTGACCACTATGTTTTAGCATG 58.675 40.000 0.00 0.00 0.00 4.06
179 181 3.694072 TGACCACTATGTTTTAGCATGGC 59.306 43.478 0.00 0.00 31.62 4.40
180 182 2.682856 ACCACTATGTTTTAGCATGGCG 59.317 45.455 0.00 0.00 31.62 5.69
181 183 2.541588 CCACTATGTTTTAGCATGGCGC 60.542 50.000 0.00 0.00 42.91 6.53
201 204 3.681897 CGCTCACTCATCTAAAAAGCAGT 59.318 43.478 0.00 0.00 0.00 4.40
204 207 5.049129 GCTCACTCATCTAAAAAGCAGTTGT 60.049 40.000 0.00 0.00 0.00 3.32
210 213 4.647424 TCTAAAAAGCAGTTGTTGGTGG 57.353 40.909 0.00 0.00 37.63 4.61
299 302 4.654091 CCAATAATGGGATGTTGACCAC 57.346 45.455 0.00 0.00 43.51 4.16
300 303 4.280819 CCAATAATGGGATGTTGACCACT 58.719 43.478 0.00 0.00 43.51 4.00
301 304 4.098349 CCAATAATGGGATGTTGACCACTG 59.902 45.833 0.00 0.00 43.51 3.66
302 305 1.549203 AATGGGATGTTGACCACTGC 58.451 50.000 0.00 0.00 40.05 4.40
303 306 0.700564 ATGGGATGTTGACCACTGCT 59.299 50.000 0.00 0.00 40.05 4.24
304 307 0.036732 TGGGATGTTGACCACTGCTC 59.963 55.000 0.00 0.00 0.00 4.26
305 308 0.678048 GGGATGTTGACCACTGCTCC 60.678 60.000 0.00 0.00 0.00 4.70
306 309 0.036732 GGATGTTGACCACTGCTCCA 59.963 55.000 0.00 0.00 0.00 3.86
307 310 1.446907 GATGTTGACCACTGCTCCAG 58.553 55.000 0.00 0.00 37.52 3.86
308 311 0.607489 ATGTTGACCACTGCTCCAGC 60.607 55.000 0.00 0.00 42.50 4.85
322 325 4.584518 CAGCATATGGGCCGGGCA 62.585 66.667 30.95 16.32 0.00 5.36
323 326 3.819652 AGCATATGGGCCGGGCAA 61.820 61.111 30.95 21.24 0.00 4.52
324 327 2.837291 GCATATGGGCCGGGCAAA 60.837 61.111 30.95 17.97 0.00 3.68
325 328 2.430610 GCATATGGGCCGGGCAAAA 61.431 57.895 30.95 15.15 0.00 2.44
326 329 1.757423 GCATATGGGCCGGGCAAAAT 61.757 55.000 30.95 20.97 0.00 1.82
327 330 1.626686 CATATGGGCCGGGCAAAATA 58.373 50.000 30.95 22.37 0.00 1.40
328 331 1.272212 CATATGGGCCGGGCAAAATAC 59.728 52.381 30.95 11.71 0.00 1.89
329 332 0.259065 TATGGGCCGGGCAAAATACA 59.741 50.000 30.95 17.47 0.00 2.29
330 333 0.616111 ATGGGCCGGGCAAAATACAA 60.616 50.000 30.95 4.40 0.00 2.41
331 334 1.216977 GGGCCGGGCAAAATACAAC 59.783 57.895 30.95 4.70 0.00 3.32
332 335 1.216977 GGCCGGGCAAAATACAACC 59.783 57.895 25.33 0.00 0.00 3.77
333 336 1.216977 GCCGGGCAAAATACAACCC 59.783 57.895 15.62 0.00 39.12 4.11
334 337 1.536943 GCCGGGCAAAATACAACCCA 61.537 55.000 15.62 0.00 42.97 4.51
335 338 0.969894 CCGGGCAAAATACAACCCAA 59.030 50.000 0.00 0.00 42.97 4.12
336 339 1.552792 CCGGGCAAAATACAACCCAAT 59.447 47.619 0.00 0.00 42.97 3.16
337 340 2.761208 CCGGGCAAAATACAACCCAATA 59.239 45.455 0.00 0.00 42.97 1.90
338 341 3.195825 CCGGGCAAAATACAACCCAATAA 59.804 43.478 0.00 0.00 42.97 1.40
339 342 4.141824 CCGGGCAAAATACAACCCAATAAT 60.142 41.667 0.00 0.00 42.97 1.28
340 343 5.047188 CGGGCAAAATACAACCCAATAATC 58.953 41.667 0.00 0.00 42.97 1.75
341 344 5.163457 CGGGCAAAATACAACCCAATAATCT 60.163 40.000 0.00 0.00 42.97 2.40
342 345 6.039941 CGGGCAAAATACAACCCAATAATCTA 59.960 38.462 0.00 0.00 42.97 1.98
343 346 7.255801 CGGGCAAAATACAACCCAATAATCTAT 60.256 37.037 0.00 0.00 42.97 1.98
344 347 9.084533 GGGCAAAATACAACCCAATAATCTATA 57.915 33.333 0.00 0.00 42.33 1.31
465 468 8.947055 ACTAAAAGTGCATTTCAAGAATGTTT 57.053 26.923 9.56 0.00 0.00 2.83
466 469 8.819974 ACTAAAAGTGCATTTCAAGAATGTTTG 58.180 29.630 9.56 0.00 0.00 2.93
557 561 4.982295 TCTTCAAGAAGTGTCGTGTACATG 59.018 41.667 8.90 8.90 41.10 3.21
566 570 4.986659 AGTGTCGTGTACATGGTAGAAAAC 59.013 41.667 15.02 4.76 41.10 2.43
568 572 5.118203 GTGTCGTGTACATGGTAGAAAACTC 59.882 44.000 15.02 1.93 41.10 3.01
575 579 8.230486 GTGTACATGGTAGAAAACTCAATGAAG 58.770 37.037 0.00 0.00 0.00 3.02
645 649 7.789759 CGAATCAGATGTTTATAGAAGCGTTTC 59.210 37.037 3.49 3.49 0.00 2.78
647 651 7.290857 TCAGATGTTTATAGAAGCGTTTCAC 57.709 36.000 14.70 3.82 35.70 3.18
682 686 9.856488 TTCACTCATTTTAGTCTGTATGTAGTC 57.144 33.333 0.00 0.00 0.00 2.59
739 743 5.621193 ACGGAAGGAATAATAATGACCTGG 58.379 41.667 0.00 0.00 0.00 4.45
788 792 2.197792 AAAAACGAAAACCGGCTGAC 57.802 45.000 0.00 0.00 43.93 3.51
825 829 1.477014 GCTGGCCCAGAGTATTTACCC 60.477 57.143 16.85 0.00 32.44 3.69
826 830 0.834612 TGGCCCAGAGTATTTACCCG 59.165 55.000 0.00 0.00 0.00 5.28
1102 1119 3.764466 CCCGCACTCTCCGCTTCT 61.764 66.667 0.00 0.00 0.00 2.85
1461 1515 6.048732 TGTAGTGTTTGATGATGAAGGCTA 57.951 37.500 0.00 0.00 0.00 3.93
1519 1573 4.638865 CCTTAAGGGTTGGTTGCTATACAC 59.361 45.833 14.25 0.00 0.00 2.90
1526 1580 6.321181 AGGGTTGGTTGCTATACACAAATATG 59.679 38.462 0.00 0.00 0.00 1.78
1528 1582 7.363443 GGGTTGGTTGCTATACACAAATATGTT 60.363 37.037 0.00 0.00 37.82 2.71
1529 1583 7.487829 GGTTGGTTGCTATACACAAATATGTTG 59.512 37.037 0.00 0.00 37.82 3.33
1533 1587 6.375945 TGCTATACACAAATATGTTGGCTG 57.624 37.500 0.00 0.00 37.82 4.85
1652 3363 3.916359 ATCTCTCTACCAGTCGACTGA 57.084 47.619 40.21 23.93 46.59 3.41
1653 3364 3.254470 TCTCTCTACCAGTCGACTGAG 57.746 52.381 40.21 30.63 46.59 3.35
1654 3365 2.832733 TCTCTCTACCAGTCGACTGAGA 59.167 50.000 40.21 32.53 46.59 3.27
1655 3366 3.452990 TCTCTCTACCAGTCGACTGAGAT 59.547 47.826 40.21 27.76 46.59 2.75
1656 3367 4.080807 TCTCTCTACCAGTCGACTGAGATT 60.081 45.833 40.21 24.73 46.59 2.40
1657 3368 4.590918 TCTCTACCAGTCGACTGAGATTT 58.409 43.478 40.21 22.60 46.59 2.17
1658 3369 5.742063 TCTCTACCAGTCGACTGAGATTTA 58.258 41.667 40.21 22.05 46.59 1.40
1659 3370 6.178324 TCTCTACCAGTCGACTGAGATTTAA 58.822 40.000 40.21 20.03 46.59 1.52
1660 3371 6.316640 TCTCTACCAGTCGACTGAGATTTAAG 59.683 42.308 40.21 26.25 46.59 1.85
1661 3372 3.851098 ACCAGTCGACTGAGATTTAAGC 58.149 45.455 40.21 0.00 46.59 3.09
1662 3373 3.258372 ACCAGTCGACTGAGATTTAAGCA 59.742 43.478 40.21 0.00 46.59 3.91
1663 3374 4.245660 CCAGTCGACTGAGATTTAAGCAA 58.754 43.478 40.21 0.00 46.59 3.91
1664 3375 4.328440 CCAGTCGACTGAGATTTAAGCAAG 59.672 45.833 40.21 18.75 46.59 4.01
1665 3376 4.926238 CAGTCGACTGAGATTTAAGCAAGT 59.074 41.667 36.73 0.00 46.59 3.16
1666 3377 5.061560 CAGTCGACTGAGATTTAAGCAAGTC 59.938 44.000 36.73 6.15 46.59 3.01
1667 3378 5.047660 AGTCGACTGAGATTTAAGCAAGTCT 60.048 40.000 19.30 0.00 33.74 3.24
1668 3379 5.287513 GTCGACTGAGATTTAAGCAAGTCTC 59.712 44.000 8.70 3.23 44.01 3.36
1673 3384 6.101650 TGAGATTTAAGCAAGTCTCAGTCA 57.898 37.500 7.61 0.00 46.61 3.41
1674 3385 6.524734 TGAGATTTAAGCAAGTCTCAGTCAA 58.475 36.000 7.61 0.00 46.61 3.18
1675 3386 6.648310 TGAGATTTAAGCAAGTCTCAGTCAAG 59.352 38.462 7.61 0.00 46.61 3.02
1676 3387 6.529220 AGATTTAAGCAAGTCTCAGTCAAGT 58.471 36.000 0.00 0.00 0.00 3.16
1677 3388 5.991328 TTTAAGCAAGTCTCAGTCAAGTG 57.009 39.130 0.00 0.00 0.00 3.16
1678 3389 3.827008 AAGCAAGTCTCAGTCAAGTGA 57.173 42.857 0.00 0.00 0.00 3.41
1679 3390 3.104843 AGCAAGTCTCAGTCAAGTGAC 57.895 47.619 3.12 3.12 45.08 3.67
1693 3404 6.680055 GTCAAGTGACATAACATGCAAAAG 57.320 37.500 6.57 0.00 44.18 2.27
1774 3485 6.581919 CAGATATAGCATCGACTGAGACTTTG 59.418 42.308 0.00 0.00 0.00 2.77
1835 3546 8.948631 TTGACATACTACTTGAGGATTTGATC 57.051 34.615 0.00 0.00 0.00 2.92
2508 4219 4.274214 TGATTCAATTTAGATGAGGCAGCG 59.726 41.667 0.00 0.00 0.00 5.18
2631 4342 7.404671 TGTAGCTACATGAGAAAGTATGTGA 57.595 36.000 22.67 0.00 37.98 3.58
2652 4363 4.696877 TGATGCATGAAGTGAGAAAATCGT 59.303 37.500 2.46 0.00 0.00 3.73
2692 4403 9.586435 AAGGTTCAACTCAGAAAAGTAAAATTG 57.414 29.630 0.00 0.00 0.00 2.32
2768 4479 2.107204 AGATGTTTCCTGTTGCCTCAGT 59.893 45.455 4.89 0.00 34.02 3.41
2867 4578 1.869767 CTGTGCTCAAGAGTGTTCACC 59.130 52.381 0.00 0.00 31.60 4.02
3131 4843 7.556275 TGGCAATCAATCTTTACTAGTTTAGGG 59.444 37.037 0.00 0.00 0.00 3.53
3221 4933 5.564550 AGCAATGACTCAACCTGTATCTTT 58.435 37.500 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 6.873605 CCTATCTATTTGACGCACCATCATAA 59.126 38.462 0.00 0.00 0.00 1.90
32 33 6.210584 TCCTATCTATTTGACGCACCATCATA 59.789 38.462 0.00 0.00 0.00 2.15
33 34 5.012046 TCCTATCTATTTGACGCACCATCAT 59.988 40.000 0.00 0.00 0.00 2.45
34 35 4.343814 TCCTATCTATTTGACGCACCATCA 59.656 41.667 0.00 0.00 0.00 3.07
35 36 4.883083 TCCTATCTATTTGACGCACCATC 58.117 43.478 0.00 0.00 0.00 3.51
36 37 4.955811 TCCTATCTATTTGACGCACCAT 57.044 40.909 0.00 0.00 0.00 3.55
37 38 4.955811 ATCCTATCTATTTGACGCACCA 57.044 40.909 0.00 0.00 0.00 4.17
63 64 7.993183 GTCCCAATCCTGACTATTTTCTCATAA 59.007 37.037 0.00 0.00 0.00 1.90
65 66 6.360618 GTCCCAATCCTGACTATTTTCTCAT 58.639 40.000 0.00 0.00 0.00 2.90
66 67 5.339200 GGTCCCAATCCTGACTATTTTCTCA 60.339 44.000 0.00 0.00 0.00 3.27
78 80 0.839946 AATCGGAGGTCCCAATCCTG 59.160 55.000 0.00 0.00 35.20 3.86
117 119 2.014128 GTGTGCCTGTTATAACGCCAT 58.986 47.619 10.92 0.00 0.00 4.40
120 122 1.201877 CGTGTGTGCCTGTTATAACGC 60.202 52.381 10.92 9.41 0.00 4.84
144 146 1.348036 AGTGGTCAAAGGGTGTAGAGC 59.652 52.381 0.00 0.00 0.00 4.09
173 175 0.249615 TAGATGAGTGAGCGCCATGC 60.250 55.000 2.29 0.00 46.98 4.06
174 176 2.229675 TTAGATGAGTGAGCGCCATG 57.770 50.000 2.29 0.00 0.00 3.66
175 177 2.988010 TTTAGATGAGTGAGCGCCAT 57.012 45.000 2.29 0.00 0.00 4.40
176 178 2.760634 TTTTAGATGAGTGAGCGCCA 57.239 45.000 2.29 0.00 0.00 5.69
177 179 2.223135 GCTTTTTAGATGAGTGAGCGCC 60.223 50.000 2.29 0.00 0.00 6.53
179 181 3.681897 ACTGCTTTTTAGATGAGTGAGCG 59.318 43.478 0.00 0.00 0.00 5.03
180 182 5.049129 ACAACTGCTTTTTAGATGAGTGAGC 60.049 40.000 0.00 0.00 0.00 4.26
181 183 6.551385 ACAACTGCTTTTTAGATGAGTGAG 57.449 37.500 0.00 0.00 0.00 3.51
182 184 6.238731 CCAACAACTGCTTTTTAGATGAGTGA 60.239 38.462 0.00 0.00 0.00 3.41
183 185 5.916883 CCAACAACTGCTTTTTAGATGAGTG 59.083 40.000 0.00 0.00 0.00 3.51
184 186 5.594317 ACCAACAACTGCTTTTTAGATGAGT 59.406 36.000 0.00 0.00 0.00 3.41
278 281 4.098349 CAGTGGTCAACATCCCATTATTGG 59.902 45.833 0.00 0.00 43.23 3.16
279 282 4.440525 GCAGTGGTCAACATCCCATTATTG 60.441 45.833 0.00 0.00 32.32 1.90
280 283 3.701040 GCAGTGGTCAACATCCCATTATT 59.299 43.478 0.00 0.00 32.32 1.40
281 284 3.053395 AGCAGTGGTCAACATCCCATTAT 60.053 43.478 0.00 0.00 32.32 1.28
282 285 2.308570 AGCAGTGGTCAACATCCCATTA 59.691 45.455 0.00 0.00 32.32 1.90
283 286 1.076024 AGCAGTGGTCAACATCCCATT 59.924 47.619 0.00 0.00 32.32 3.16
284 287 0.700564 AGCAGTGGTCAACATCCCAT 59.299 50.000 0.00 0.00 32.32 4.00
285 288 0.036732 GAGCAGTGGTCAACATCCCA 59.963 55.000 17.32 0.00 0.00 4.37
286 289 0.678048 GGAGCAGTGGTCAACATCCC 60.678 60.000 22.95 1.45 0.00 3.85
287 290 0.036732 TGGAGCAGTGGTCAACATCC 59.963 55.000 22.95 6.60 0.00 3.51
288 291 1.446907 CTGGAGCAGTGGTCAACATC 58.553 55.000 22.95 6.62 0.00 3.06
289 292 0.607489 GCTGGAGCAGTGGTCAACAT 60.607 55.000 22.95 0.00 41.59 2.71
290 293 1.227943 GCTGGAGCAGTGGTCAACA 60.228 57.895 22.95 12.04 41.59 3.33
291 294 3.660621 GCTGGAGCAGTGGTCAAC 58.339 61.111 22.95 8.02 41.59 3.18
305 308 4.584518 TGCCCGGCCCATATGCTG 62.585 66.667 7.03 0.00 37.37 4.41
306 309 2.870035 TTTTGCCCGGCCCATATGCT 62.870 55.000 7.03 0.00 0.00 3.79
307 310 1.757423 ATTTTGCCCGGCCCATATGC 61.757 55.000 7.03 0.00 0.00 3.14
308 311 1.272212 GTATTTTGCCCGGCCCATATG 59.728 52.381 7.03 0.00 0.00 1.78
309 312 1.133325 TGTATTTTGCCCGGCCCATAT 60.133 47.619 7.03 0.00 0.00 1.78
310 313 0.259065 TGTATTTTGCCCGGCCCATA 59.741 50.000 7.03 0.00 0.00 2.74
311 314 0.616111 TTGTATTTTGCCCGGCCCAT 60.616 50.000 7.03 0.00 0.00 4.00
312 315 1.228894 TTGTATTTTGCCCGGCCCA 60.229 52.632 7.03 0.00 0.00 5.36
313 316 1.216977 GTTGTATTTTGCCCGGCCC 59.783 57.895 7.03 0.00 0.00 5.80
314 317 1.216977 GGTTGTATTTTGCCCGGCC 59.783 57.895 7.03 0.00 0.00 6.13
315 318 1.216977 GGGTTGTATTTTGCCCGGC 59.783 57.895 1.04 1.04 0.00 6.13
316 319 0.969894 TTGGGTTGTATTTTGCCCGG 59.030 50.000 0.00 0.00 43.89 5.73
317 320 4.457834 TTATTGGGTTGTATTTTGCCCG 57.542 40.909 0.00 0.00 43.89 6.13
318 321 6.233905 AGATTATTGGGTTGTATTTTGCCC 57.766 37.500 0.00 0.00 41.42 5.36
450 453 9.850628 AGATACATGACAAACATTCTTGAAATG 57.149 29.630 0.00 0.00 37.07 2.32
548 552 6.367695 TCATTGAGTTTTCTACCATGTACACG 59.632 38.462 0.00 0.00 0.00 4.49
619 623 6.755461 ACGCTTCTATAAACATCTGATTCG 57.245 37.500 0.00 0.00 0.00 3.34
625 629 6.874134 ACAGTGAAACGCTTCTATAAACATCT 59.126 34.615 0.00 0.00 45.86 2.90
638 642 2.486203 TGAACAAACACAGTGAAACGCT 59.514 40.909 7.81 0.00 45.86 5.07
645 649 7.250569 ACTAAAATGAGTGAACAAACACAGTG 58.749 34.615 0.00 0.00 42.45 3.66
647 651 7.641411 CAGACTAAAATGAGTGAACAAACACAG 59.359 37.037 0.00 0.00 42.45 3.66
713 717 6.365247 CAGGTCATTATTATTCCTTCCGTACG 59.635 42.308 8.69 8.69 0.00 3.67
772 776 1.096416 TTTGTCAGCCGGTTTTCGTT 58.904 45.000 1.90 0.00 37.11 3.85
773 777 1.096416 TTTTGTCAGCCGGTTTTCGT 58.904 45.000 1.90 0.00 37.11 3.85
774 778 1.472990 GTTTTGTCAGCCGGTTTTCG 58.527 50.000 1.90 0.00 38.88 3.46
775 779 1.847818 GGTTTTGTCAGCCGGTTTTC 58.152 50.000 1.90 0.00 0.00 2.29
781 785 2.343163 TTTGCCGGTTTTGTCAGCCG 62.343 55.000 1.90 0.00 44.55 5.52
782 786 0.033366 ATTTGCCGGTTTTGTCAGCC 59.967 50.000 1.90 0.00 0.00 4.85
783 787 1.139163 CATTTGCCGGTTTTGTCAGC 58.861 50.000 1.90 0.00 0.00 4.26
784 788 1.605202 CCCATTTGCCGGTTTTGTCAG 60.605 52.381 1.90 0.00 0.00 3.51
785 789 0.390860 CCCATTTGCCGGTTTTGTCA 59.609 50.000 1.90 0.00 0.00 3.58
786 790 0.320334 CCCCATTTGCCGGTTTTGTC 60.320 55.000 1.90 0.00 0.00 3.18
787 791 1.751563 CCCCATTTGCCGGTTTTGT 59.248 52.632 1.90 0.00 0.00 2.83
788 792 1.670730 GCCCCATTTGCCGGTTTTG 60.671 57.895 1.90 0.00 0.00 2.44
851 857 3.074412 ACAAATTGGACTAGTTGCTCCG 58.926 45.455 0.00 0.00 0.00 4.63
911 928 1.546476 TCTTCTTCTCGAACTGGGCTC 59.454 52.381 0.00 0.00 0.00 4.70
1195 1212 2.991540 GGGCAAAGTCTGGGTGGC 60.992 66.667 0.00 0.00 37.12 5.01
1461 1515 5.874093 AGAAGAAACCATGATCACTTCAGT 58.126 37.500 18.41 2.72 37.89 3.41
1519 1573 2.159393 CGTGGGACAGCCAACATATTTG 60.159 50.000 0.00 0.00 41.80 2.32
1526 1580 2.668550 GACCGTGGGACAGCCAAC 60.669 66.667 0.00 0.00 41.80 3.77
1528 1582 2.847234 AAGACCGTGGGACAGCCA 60.847 61.111 0.00 0.00 41.80 4.75
1529 1583 2.358737 CAAGACCGTGGGACAGCC 60.359 66.667 0.00 0.00 41.80 4.85
1533 1587 1.479323 TGTATAGCAAGACCGTGGGAC 59.521 52.381 0.00 0.00 0.00 4.46
1652 3363 6.426328 CACTTGACTGAGACTTGCTTAAATCT 59.574 38.462 0.00 0.00 0.00 2.40
1653 3364 6.425114 TCACTTGACTGAGACTTGCTTAAATC 59.575 38.462 0.00 0.00 0.00 2.17
1654 3365 6.203723 GTCACTTGACTGAGACTTGCTTAAAT 59.796 38.462 1.92 0.00 41.65 1.40
1655 3366 5.523916 GTCACTTGACTGAGACTTGCTTAAA 59.476 40.000 1.92 0.00 41.65 1.52
1656 3367 5.050490 GTCACTTGACTGAGACTTGCTTAA 58.950 41.667 1.92 0.00 41.65 1.85
1657 3368 4.099419 TGTCACTTGACTGAGACTTGCTTA 59.901 41.667 10.63 0.00 44.99 3.09
1658 3369 3.118629 TGTCACTTGACTGAGACTTGCTT 60.119 43.478 10.63 0.00 44.99 3.91
1659 3370 2.432146 TGTCACTTGACTGAGACTTGCT 59.568 45.455 10.63 0.00 44.99 3.91
1660 3371 2.826428 TGTCACTTGACTGAGACTTGC 58.174 47.619 10.63 0.00 44.99 4.01
1661 3372 5.985530 TGTTATGTCACTTGACTGAGACTTG 59.014 40.000 10.63 0.00 44.99 3.16
1662 3373 6.161855 TGTTATGTCACTTGACTGAGACTT 57.838 37.500 10.63 0.00 44.99 3.01
1663 3374 5.791336 TGTTATGTCACTTGACTGAGACT 57.209 39.130 10.63 0.00 44.99 3.24
1664 3375 5.163913 GCATGTTATGTCACTTGACTGAGAC 60.164 44.000 10.63 5.26 44.99 3.36
1665 3376 4.931601 GCATGTTATGTCACTTGACTGAGA 59.068 41.667 10.63 0.00 44.99 3.27
1666 3377 4.692155 TGCATGTTATGTCACTTGACTGAG 59.308 41.667 10.63 0.00 44.99 3.35
1667 3378 4.640364 TGCATGTTATGTCACTTGACTGA 58.360 39.130 10.63 0.00 44.99 3.41
1668 3379 5.361135 TTGCATGTTATGTCACTTGACTG 57.639 39.130 10.63 1.04 44.99 3.51
1669 3380 6.262944 TCTTTTGCATGTTATGTCACTTGACT 59.737 34.615 10.63 0.00 44.99 3.41
1670 3381 6.437928 TCTTTTGCATGTTATGTCACTTGAC 58.562 36.000 2.19 2.19 44.97 3.18
1671 3382 6.486320 TCTCTTTTGCATGTTATGTCACTTGA 59.514 34.615 0.00 0.00 0.00 3.02
1672 3383 6.671190 TCTCTTTTGCATGTTATGTCACTTG 58.329 36.000 0.00 0.00 0.00 3.16
1673 3384 6.882610 TCTCTTTTGCATGTTATGTCACTT 57.117 33.333 0.00 0.00 0.00 3.16
1674 3385 6.882610 TTCTCTTTTGCATGTTATGTCACT 57.117 33.333 0.00 0.00 0.00 3.41
1675 3386 7.928908 TTTTCTCTTTTGCATGTTATGTCAC 57.071 32.000 0.00 0.00 0.00 3.67
1676 3387 8.412456 TCTTTTTCTCTTTTGCATGTTATGTCA 58.588 29.630 0.00 0.00 0.00 3.58
1677 3388 8.801715 TCTTTTTCTCTTTTGCATGTTATGTC 57.198 30.769 0.00 0.00 0.00 3.06
1678 3389 9.598517 TTTCTTTTTCTCTTTTGCATGTTATGT 57.401 25.926 0.00 0.00 0.00 2.29
1785 3496 3.189702 AGTCTTGCTAAGTCTCAGTCGAC 59.810 47.826 7.70 7.70 0.00 4.20
1835 3546 4.323417 TGCAACCTGTAGAAATAGGTGTG 58.677 43.478 0.00 0.00 45.79 3.82
1947 3658 2.203294 GCAACGTTCCCTGGTGGT 60.203 61.111 0.00 0.00 34.77 4.16
2508 4219 3.377172 ACCAGCAAGTTTCACAGTACAAC 59.623 43.478 0.00 0.00 0.00 3.32
2631 4342 5.396484 CAACGATTTTCTCACTTCATGCAT 58.604 37.500 0.00 0.00 0.00 3.96
2652 4363 6.601332 AGTTGAACCTTAGAACTCAATCCAA 58.399 36.000 0.00 0.00 30.96 3.53
2806 4517 5.817616 CACTTGAAGTGCAAATAGCTTTG 57.182 39.130 12.89 0.00 45.94 2.77
2867 4578 4.695455 AGATCCAAACACTTCGGTAACATG 59.305 41.667 0.00 0.00 0.00 3.21
3107 4819 8.732746 TCCCTAAACTAGTAAAGATTGATTGC 57.267 34.615 0.00 0.00 0.00 3.56
3131 4843 4.273148 TCTTGCCTCCAGTAGAAACTTC 57.727 45.455 0.00 0.00 31.97 3.01
3221 4933 4.067896 GGAGTGCTCAGAACTGAATCAAA 58.932 43.478 0.00 0.00 39.39 2.69
3323 5036 0.183014 ATGATGGCTTCTGCTGGAGG 59.817 55.000 0.52 0.00 39.59 4.30


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

AutoCloner maintained by Alex Coulton.