Multiple sequence alignment - TraesCS1A01G259200

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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 TraesCS1A01G259200 chr1A 100.000 4551 0 0 1 4551 452284710 452280160 0.000000e+00 8405
1 TraesCS1A01G259200 chr1B 92.184 4593 202 69 4 4546 474121548 474117063 0.000000e+00 6348
2 TraesCS1A01G259200 chr1B 94.068 118 4 2 2298 2415 573578298 573578184 4.680000e-40 176
3 TraesCS1A01G259200 chr1D 93.295 4325 146 60 268 4546 351443030 351438804 0.000000e+00 6248
4 TraesCS1A01G259200 chr1D 95.580 181 7 1 1 181 351443261 351443082 5.760000e-74 289
5 TraesCS1A01G259200 chr3B 84.767 407 51 6 1409 1815 705151932 705152327 9.170000e-107 398
6 TraesCS1A01G259200 chr3D 85.199 277 23 8 3279 3540 532938005 532938278 7.500000e-68 268
7 TraesCS1A01G259200 chr3A 87.981 208 13 6 3342 3540 668688056 668688260 7.610000e-58 235
8 TraesCS1A01G259200 chr3A 84.647 241 26 7 2730 2960 668686670 668686909 3.540000e-56 230


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 TraesCS1A01G259200 chr1A 452280160 452284710 4550 True 8405.0 8405 100.0000 1 4551 1 chr1A.!!$R1 4550
1 TraesCS1A01G259200 chr1B 474117063 474121548 4485 True 6348.0 6348 92.1840 4 4546 1 chr1B.!!$R1 4542
2 TraesCS1A01G259200 chr1D 351438804 351443261 4457 True 3268.5 6248 94.4375 1 4546 2 chr1D.!!$R1 4545
3 TraesCS1A01G259200 chr3A 668686670 668688260 1590 False 232.5 235 86.3140 2730 3540 2 chr3A.!!$F1 810

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
107 108 0.038618 CCGCTAAACAAAACCAGGGC 60.039 55.0 0.00 0.0 0.00 5.19 F
209 229 0.177604 CGCTCCCTTCTGCAGAATCT 59.822 55.0 28.57 0.0 33.01 2.40 F
1359 1423 0.322322 AGGACGACGACTCTGACTCT 59.678 55.0 0.00 0.0 0.00 3.24 F
3081 3171 0.318762 AGACTCAGGAACACTTCGGC 59.681 55.0 0.00 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1333 0.249868 TGTCGACCTTGCAGTCCTTG 60.250 55.000 14.12 0.0 32.91 3.61 R
1703 1777 0.320683 CATCCGACTGCAAGACACCA 60.321 55.000 0.00 0.0 37.43 4.17 R
3307 3495 1.001633 GCTTCCTGGTAACGTTCCTGA 59.998 52.381 2.82 5.0 42.51 3.86 R
4522 5526 0.464452 ATAGCTGGTAACGCTGACCC 59.536 55.000 0.00 0.0 44.17 4.46 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
80 81 7.328737 AGTAGTTAATGCCAGTACCAAACTAG 58.671 38.462 0.00 0.00 35.76 2.57
85 86 9.257651 GTTAATGCCAGTACCAAACTAGTATAG 57.742 37.037 0.00 0.00 46.50 1.31
86 87 5.272283 TGCCAGTACCAAACTAGTATAGC 57.728 43.478 0.00 0.00 44.39 2.97
89 90 5.598769 CCAGTACCAAACTAGTATAGCACC 58.401 45.833 0.00 0.00 44.39 5.01
107 108 0.038618 CCGCTAAACAAAACCAGGGC 60.039 55.000 0.00 0.00 0.00 5.19
154 155 2.278206 CATGTCGACTCGGCTCGG 60.278 66.667 17.92 0.00 34.27 4.63
204 224 4.479993 CCCCGCTCCCTTCTGCAG 62.480 72.222 7.63 7.63 0.00 4.41
205 225 3.393970 CCCGCTCCCTTCTGCAGA 61.394 66.667 13.74 13.74 0.00 4.26
206 226 2.665000 CCGCTCCCTTCTGCAGAA 59.335 61.111 26.87 26.87 0.00 3.02
207 227 1.222936 CCGCTCCCTTCTGCAGAAT 59.777 57.895 28.57 0.00 33.01 2.40
208 228 0.813210 CCGCTCCCTTCTGCAGAATC 60.813 60.000 28.57 14.18 33.01 2.52
209 229 0.177604 CGCTCCCTTCTGCAGAATCT 59.822 55.000 28.57 0.00 33.01 2.40
210 230 1.410517 CGCTCCCTTCTGCAGAATCTA 59.589 52.381 28.57 15.41 33.01 1.98
211 231 2.036992 CGCTCCCTTCTGCAGAATCTAT 59.963 50.000 28.57 0.00 33.01 1.98
212 232 3.663025 GCTCCCTTCTGCAGAATCTATC 58.337 50.000 28.57 14.42 33.01 2.08
213 233 3.324556 GCTCCCTTCTGCAGAATCTATCT 59.675 47.826 28.57 0.00 39.68 1.98
214 234 4.526262 GCTCCCTTCTGCAGAATCTATCTA 59.474 45.833 28.57 4.91 36.32 1.98
232 252 3.870559 TCTACAGAAGGAAAAGGAGGGT 58.129 45.455 0.00 0.00 0.00 4.34
235 255 2.108425 ACAGAAGGAAAAGGAGGGTTCC 59.892 50.000 0.00 0.00 43.17 3.62
243 263 4.452733 GGAGGGTTCCTGCGACCG 62.453 72.222 0.00 0.00 40.58 4.79
265 285 1.336755 TGCCAAAGGAAAAGAAGCGAC 59.663 47.619 0.00 0.00 0.00 5.19
266 286 1.335964 GCCAAAGGAAAAGAAGCGACC 60.336 52.381 0.00 0.00 0.00 4.79
312 337 0.447011 TTTACCGCGCGTATTTTGGG 59.553 50.000 29.95 13.09 0.00 4.12
347 381 4.222847 GGAGGGGTCGTCGCATCC 62.223 72.222 13.76 13.76 46.59 3.51
348 382 3.458163 GAGGGGTCGTCGCATCCA 61.458 66.667 0.20 0.00 32.53 3.41
350 384 3.771160 GGGGTCGTCGCATCCAGT 61.771 66.667 0.00 0.00 0.00 4.00
351 385 2.420568 GGGGTCGTCGCATCCAGTA 61.421 63.158 0.00 0.00 0.00 2.74
352 386 1.226888 GGGTCGTCGCATCCAGTAC 60.227 63.158 0.00 0.00 0.00 2.73
353 387 1.664321 GGGTCGTCGCATCCAGTACT 61.664 60.000 0.00 0.00 0.00 2.73
367 401 2.492484 CCAGTACTGGTAGCTCTCGTTT 59.508 50.000 30.57 0.00 45.53 3.60
592 630 1.612442 TCTTCTTCCTCCCACCCCG 60.612 63.158 0.00 0.00 0.00 5.73
689 727 2.464459 CCGCCGCAGAAATCCTCAC 61.464 63.158 0.00 0.00 0.00 3.51
719 757 4.952102 TTGGGGGCCAAGCAACCC 62.952 66.667 4.39 5.10 44.12 4.11
728 776 1.898574 CAAGCAACCCAGCGAACCT 60.899 57.895 0.00 0.00 40.15 3.50
743 791 2.727298 CGAACCTAACTCGACTCGGTTC 60.727 54.545 15.77 15.77 46.25 3.62
756 804 2.159544 ACTCGGTTCTCTCGATTCGTTC 60.160 50.000 5.89 0.00 36.01 3.95
758 806 1.132643 CGGTTCTCTCGATTCGTTCCT 59.867 52.381 5.89 0.00 0.00 3.36
761 809 1.464734 TCTCTCGATTCGTTCCTGCT 58.535 50.000 5.89 0.00 0.00 4.24
764 812 1.475441 CTCGATTCGTTCCTGCTCGC 61.475 60.000 5.89 0.00 0.00 5.03
765 813 2.517450 CGATTCGTTCCTGCTCGCC 61.517 63.158 0.00 0.00 0.00 5.54
766 814 2.125106 ATTCGTTCCTGCTCGCCC 60.125 61.111 0.00 0.00 0.00 6.13
777 840 4.468689 CTCGCCCCTCCCCGTTTC 62.469 72.222 0.00 0.00 0.00 2.78
790 853 3.438781 TCCCCGTTTCTCGATTTGATTTG 59.561 43.478 0.00 0.00 42.86 2.32
791 854 3.438781 CCCCGTTTCTCGATTTGATTTGA 59.561 43.478 0.00 0.00 42.86 2.69
793 856 5.295787 CCCCGTTTCTCGATTTGATTTGATA 59.704 40.000 0.00 0.00 42.86 2.15
794 857 6.017109 CCCCGTTTCTCGATTTGATTTGATAT 60.017 38.462 0.00 0.00 42.86 1.63
795 858 7.417612 CCCGTTTCTCGATTTGATTTGATATT 58.582 34.615 0.00 0.00 42.86 1.28
796 859 7.915397 CCCGTTTCTCGATTTGATTTGATATTT 59.085 33.333 0.00 0.00 42.86 1.40
797 860 9.289303 CCGTTTCTCGATTTGATTTGATATTTT 57.711 29.630 0.00 0.00 42.86 1.82
824 887 2.094383 GAATTTCGCTTTCACGATCGC 58.906 47.619 16.60 0.00 42.54 4.58
906 969 6.578691 GGCGTAGTAGTAATAATTTCGCAAG 58.421 40.000 16.49 0.00 42.27 4.01
907 970 6.346359 GGCGTAGTAGTAATAATTTCGCAAGG 60.346 42.308 16.49 0.00 42.27 3.61
908 971 6.346359 GCGTAGTAGTAATAATTTCGCAAGGG 60.346 42.308 12.26 0.00 40.63 3.95
909 972 6.145048 CGTAGTAGTAATAATTTCGCAAGGGG 59.855 42.308 0.00 0.00 38.47 4.79
950 1013 2.670635 CGGAGCATCGGTTCTTCTG 58.329 57.895 0.00 0.00 34.37 3.02
953 1016 1.363744 GAGCATCGGTTCTTCTGGTG 58.636 55.000 0.00 0.00 36.67 4.17
976 1039 1.439679 CTAGCTGTTTGTTCCCGTCC 58.560 55.000 0.00 0.00 0.00 4.79
977 1040 1.002087 CTAGCTGTTTGTTCCCGTCCT 59.998 52.381 0.00 0.00 0.00 3.85
978 1041 0.535102 AGCTGTTTGTTCCCGTCCTG 60.535 55.000 0.00 0.00 0.00 3.86
979 1042 0.818040 GCTGTTTGTTCCCGTCCTGT 60.818 55.000 0.00 0.00 0.00 4.00
981 1044 1.098712 TGTTTGTTCCCGTCCTGTGC 61.099 55.000 0.00 0.00 0.00 4.57
1353 1417 2.047083 AGCGAGGACGACGACTCT 60.047 61.111 17.42 5.66 42.66 3.24
1359 1423 0.322322 AGGACGACGACTCTGACTCT 59.678 55.000 0.00 0.00 0.00 3.24
1439 1512 0.323542 GACAACGAGGAGGAGGAGGA 60.324 60.000 0.00 0.00 0.00 3.71
1440 1513 0.323908 ACAACGAGGAGGAGGAGGAG 60.324 60.000 0.00 0.00 0.00 3.69
1441 1514 1.040339 CAACGAGGAGGAGGAGGAGG 61.040 65.000 0.00 0.00 0.00 4.30
1482 1555 3.311110 GAGGAGGACCACCACGCA 61.311 66.667 10.90 0.00 38.94 5.24
1564 1637 1.899437 GCAGATCGTTGGGGAGGTCA 61.899 60.000 0.00 0.00 0.00 4.02
1636 1709 3.490439 TCTGTGCACTTCTTCCATTCA 57.510 42.857 19.41 0.00 0.00 2.57
1637 1710 4.025040 TCTGTGCACTTCTTCCATTCAT 57.975 40.909 19.41 0.00 0.00 2.57
1665 1738 6.770785 TGCTAAACCTGTTATTTGTCAACTCT 59.229 34.615 0.00 0.00 0.00 3.24
1703 1777 8.362639 AGCATTGATCTGAACTAAAACACAAAT 58.637 29.630 0.00 0.00 0.00 2.32
1793 1871 3.887716 TCTCCACGCTTAAGGTACCTATC 59.112 47.826 16.67 3.78 0.00 2.08
1862 1940 2.905415 ATCTTTGGGGCTGTTCATCA 57.095 45.000 0.00 0.00 0.00 3.07
1871 1949 2.551071 GGGCTGTTCATCATAGGCTACC 60.551 54.545 0.00 0.00 37.20 3.18
1979 2057 8.515414 GCTTCATGAACTTTTATCTAGTTTGGT 58.485 33.333 3.38 0.00 36.04 3.67
2081 2162 1.748122 CCAGTCCATCTGCACTGCC 60.748 63.158 0.00 0.00 42.38 4.85
2086 2167 0.678684 TCCATCTGCACTGCCACATG 60.679 55.000 0.00 0.00 0.00 3.21
2107 2188 3.566322 TGGTCACCATTTACCTTTGTTCG 59.434 43.478 0.00 0.00 36.67 3.95
2282 2363 5.415701 TGCAGGTAAAGGATCTGAATTTGTC 59.584 40.000 0.00 0.00 38.77 3.18
2325 2406 9.605275 CATCCATCAGTTTCAGAGTTAATTCTA 57.395 33.333 0.00 0.00 0.00 2.10
2343 2424 9.617523 TTAATTCTATGTGAATGAATGCTCAGA 57.382 29.630 0.00 0.00 43.99 3.27
2386 2467 7.875971 ACTATATTATTGCTGCTTTTACCTGC 58.124 34.615 0.00 0.00 0.00 4.85
2535 2616 8.330247 TCTCTGAGGTACTAATATATCCACTCC 58.670 40.741 4.59 0.00 41.55 3.85
2558 2639 7.394016 TCCTGCTATCTGAATTGTTTTAGTGA 58.606 34.615 0.00 0.00 0.00 3.41
2871 2961 5.305386 TGTTGAAAGAGATCAGTTCAGGAGA 59.695 40.000 0.00 0.00 33.10 3.71
3021 3111 3.459232 TCTATGAGACCAATGAAGGCG 57.541 47.619 0.00 0.00 0.00 5.52
3081 3171 0.318762 AGACTCAGGAACACTTCGGC 59.681 55.000 0.00 0.00 0.00 5.54
3152 3336 6.155827 GCTACTGAGACTTAAGCTATGATGG 58.844 44.000 1.29 0.00 0.00 3.51
3347 4323 6.128117 GGAAGCTGAAAATGGTTCGTGTTATA 60.128 38.462 0.00 0.00 41.26 0.98
3348 4324 6.178239 AGCTGAAAATGGTTCGTGTTATAC 57.822 37.500 0.00 0.00 0.00 1.47
3351 4327 6.674760 GCTGAAAATGGTTCGTGTTATACCTC 60.675 42.308 0.00 0.00 33.05 3.85
3478 4463 3.509659 GGCGACATACCAAAGCCC 58.490 61.111 0.00 0.00 41.81 5.19
3556 4541 3.880846 GGCCGGCGCTGATTCTTG 61.881 66.667 22.54 0.00 34.44 3.02
3596 4581 3.119388 CCTGATGAATTTGTCGCCATGTT 60.119 43.478 0.00 0.00 0.00 2.71
3735 4724 6.603940 TGGATGCAATAAGTTAAGCCTTTT 57.396 33.333 0.00 0.00 0.00 2.27
3890 4879 7.447238 AGGAAGCTGTAGATACTCAGATAGAAC 59.553 40.741 0.00 0.00 34.02 3.01
3969 4961 3.303329 CGTGGACATTCTTGGCATATTCG 60.303 47.826 0.00 0.00 29.63 3.34
3975 4967 4.158394 ACATTCTTGGCATATTCGTTGCTT 59.842 37.500 0.00 0.00 40.03 3.91
3992 4984 1.268079 GCTTCTTTGCAAGTCTGGACC 59.732 52.381 0.00 0.00 0.00 4.46
4109 5102 4.520111 TGTTTGGTCATGATCAGACTTTGG 59.480 41.667 25.14 0.00 36.29 3.28
4110 5103 3.354948 TGGTCATGATCAGACTTTGGG 57.645 47.619 4.01 0.00 36.29 4.12
4125 5118 0.465460 TTGGGTTCTTGCTGCTCGTT 60.465 50.000 0.00 0.00 0.00 3.85
4268 5263 1.080569 GTGCATTGCCGTTTGGGAG 60.081 57.895 6.12 0.00 36.70 4.30
4303 5298 0.109086 CAGCGTAGTGGTCAGTCAGG 60.109 60.000 0.00 0.00 0.00 3.86
4339 5334 1.032014 GCAGACAACCAAGAAAGCCA 58.968 50.000 0.00 0.00 0.00 4.75
4357 5352 1.334869 CCAGCGCACCATTTATTCCTC 59.665 52.381 11.47 0.00 0.00 3.71
4402 5397 5.389859 TGCATGTTCCAACTTCCATTAAG 57.610 39.130 0.00 0.00 41.33 1.85
4445 5449 7.739498 TTTTCTTTAGTTCGGTAGAAGCAAT 57.261 32.000 0.00 0.00 36.99 3.56
4447 5451 5.416947 TCTTTAGTTCGGTAGAAGCAATCC 58.583 41.667 0.00 0.00 36.99 3.01
4451 5455 2.678336 GTTCGGTAGAAGCAATCCAAGG 59.322 50.000 0.00 0.00 36.99 3.61
4478 5482 1.526575 CTTGTGAGCCGGCCATTGTT 61.527 55.000 26.15 1.92 0.00 2.83
4479 5483 1.523154 TTGTGAGCCGGCCATTGTTC 61.523 55.000 26.15 13.99 0.00 3.18
4480 5484 2.361104 TGAGCCGGCCATTGTTCC 60.361 61.111 26.15 2.77 0.00 3.62
4481 5485 2.361104 GAGCCGGCCATTGTTCCA 60.361 61.111 26.15 0.00 0.00 3.53
4482 5486 2.676471 AGCCGGCCATTGTTCCAC 60.676 61.111 26.15 0.00 0.00 4.02
4483 5487 3.758931 GCCGGCCATTGTTCCACC 61.759 66.667 18.11 0.00 0.00 4.61
4484 5488 2.282816 CCGGCCATTGTTCCACCA 60.283 61.111 2.24 0.00 0.00 4.17
4487 5491 1.293179 GGCCATTGTTCCACCAAGC 59.707 57.895 0.00 0.00 0.00 4.01
4496 5500 0.550914 TTCCACCAAGCAGTCTGGTT 59.449 50.000 11.52 11.52 38.82 3.67
4522 5526 3.984508 CCAGAATCTGGCAAATAGCTG 57.015 47.619 17.25 0.00 45.13 4.24
4547 5551 5.450965 GGTCAGCGTTACCAGCTATACTAAA 60.451 44.000 0.00 0.00 44.06 1.85
4548 5552 6.214399 GTCAGCGTTACCAGCTATACTAAAT 58.786 40.000 0.00 0.00 44.06 1.40
4549 5553 7.365741 GTCAGCGTTACCAGCTATACTAAATA 58.634 38.462 0.00 0.00 44.06 1.40
4550 5554 8.027771 GTCAGCGTTACCAGCTATACTAAATAT 58.972 37.037 0.00 0.00 44.06 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.667043 TGATTTACTCCATTATTATCGGCAC 57.333 36.000 0.00 0.00 0.00 5.01
80 81 4.154556 TGGTTTTGTTTAGCGGTGCTATAC 59.845 41.667 11.04 11.04 41.01 1.47
85 86 1.601914 CCTGGTTTTGTTTAGCGGTGC 60.602 52.381 0.00 0.00 0.00 5.01
86 87 1.000717 CCCTGGTTTTGTTTAGCGGTG 60.001 52.381 0.00 0.00 0.00 4.94
89 90 0.671251 TGCCCTGGTTTTGTTTAGCG 59.329 50.000 0.00 0.00 0.00 4.26
200 220 7.423844 TTTCCTTCTGTAGATAGATTCTGCA 57.576 36.000 0.00 0.00 43.77 4.41
201 221 7.440856 CCTTTTCCTTCTGTAGATAGATTCTGC 59.559 40.741 0.00 0.00 37.56 4.26
202 222 8.700051 TCCTTTTCCTTCTGTAGATAGATTCTG 58.300 37.037 0.00 0.00 35.79 3.02
203 223 8.846423 TCCTTTTCCTTCTGTAGATAGATTCT 57.154 34.615 0.00 0.00 38.57 2.40
204 224 8.147704 CCTCCTTTTCCTTCTGTAGATAGATTC 58.852 40.741 0.00 0.00 0.00 2.52
205 225 7.071824 CCCTCCTTTTCCTTCTGTAGATAGATT 59.928 40.741 0.00 0.00 0.00 2.40
206 226 6.556874 CCCTCCTTTTCCTTCTGTAGATAGAT 59.443 42.308 0.00 0.00 0.00 1.98
207 227 5.900123 CCCTCCTTTTCCTTCTGTAGATAGA 59.100 44.000 0.00 0.00 0.00 1.98
208 228 5.663556 ACCCTCCTTTTCCTTCTGTAGATAG 59.336 44.000 0.00 0.00 0.00 2.08
209 229 5.600749 ACCCTCCTTTTCCTTCTGTAGATA 58.399 41.667 0.00 0.00 0.00 1.98
210 230 4.439860 ACCCTCCTTTTCCTTCTGTAGAT 58.560 43.478 0.00 0.00 0.00 1.98
211 231 3.870559 ACCCTCCTTTTCCTTCTGTAGA 58.129 45.455 0.00 0.00 0.00 2.59
212 232 4.565861 GGAACCCTCCTTTTCCTTCTGTAG 60.566 50.000 0.00 0.00 38.65 2.74
213 233 3.329814 GGAACCCTCCTTTTCCTTCTGTA 59.670 47.826 0.00 0.00 38.65 2.74
214 234 2.108425 GGAACCCTCCTTTTCCTTCTGT 59.892 50.000 0.00 0.00 38.65 3.41
235 255 4.093952 CTTTGGCAGCGGTCGCAG 62.094 66.667 17.71 10.66 44.88 5.18
239 259 0.039165 CTTTTCCTTTGGCAGCGGTC 60.039 55.000 4.38 0.00 0.00 4.79
240 260 0.467290 TCTTTTCCTTTGGCAGCGGT 60.467 50.000 4.38 0.00 0.00 5.68
241 261 0.673437 TTCTTTTCCTTTGGCAGCGG 59.327 50.000 0.00 0.00 0.00 5.52
242 262 1.932156 GCTTCTTTTCCTTTGGCAGCG 60.932 52.381 0.00 0.00 0.00 5.18
243 263 1.788258 GCTTCTTTTCCTTTGGCAGC 58.212 50.000 0.00 0.00 0.00 5.25
244 264 1.608590 TCGCTTCTTTTCCTTTGGCAG 59.391 47.619 0.00 0.00 0.00 4.85
249 269 1.202722 TCGGGTCGCTTCTTTTCCTTT 60.203 47.619 0.00 0.00 0.00 3.11
347 381 3.851976 AAACGAGAGCTACCAGTACTG 57.148 47.619 16.34 16.34 0.00 2.74
348 382 4.587891 ACTAAACGAGAGCTACCAGTACT 58.412 43.478 0.00 0.00 0.00 2.73
350 384 5.065731 GCTAACTAAACGAGAGCTACCAGTA 59.934 44.000 0.00 0.00 0.00 2.74
351 385 4.142425 GCTAACTAAACGAGAGCTACCAGT 60.142 45.833 0.00 0.00 0.00 4.00
352 386 4.096682 AGCTAACTAAACGAGAGCTACCAG 59.903 45.833 0.00 0.00 41.60 4.00
353 387 4.015084 AGCTAACTAAACGAGAGCTACCA 58.985 43.478 0.00 0.00 41.60 3.25
363 397 1.343821 CGCCGCAGCTAACTAAACG 59.656 57.895 0.00 0.00 36.60 3.60
367 401 2.508439 GCACGCCGCAGCTAACTA 60.508 61.111 0.00 0.00 41.79 2.24
400 438 4.459089 GAGCCCACGAGGACTGCC 62.459 72.222 0.00 0.00 38.24 4.85
402 440 4.135153 CCGAGCCCACGAGGACTG 62.135 72.222 0.00 0.00 38.24 3.51
431 469 3.818787 AGGGTACGCTACGCCACG 61.819 66.667 11.28 0.00 42.01 4.94
432 470 2.202703 CAGGGTACGCTACGCCAC 60.203 66.667 12.67 0.00 42.01 5.01
433 471 4.137872 GCAGGGTACGCTACGCCA 62.138 66.667 12.67 0.00 42.01 5.69
434 472 4.886121 GGCAGGGTACGCTACGCC 62.886 72.222 20.82 20.82 42.01 5.68
532 570 4.168291 GGAGAAGGCCAGGCGAGG 62.168 72.222 5.01 0.00 0.00 4.63
719 757 1.790838 CGAGTCGAGTTAGGTTCGCTG 60.791 57.143 6.73 0.00 37.94 5.18
721 759 0.522915 CCGAGTCGAGTTAGGTTCGC 60.523 60.000 15.64 0.00 37.94 4.70
722 760 0.801251 ACCGAGTCGAGTTAGGTTCG 59.199 55.000 15.64 3.21 39.33 3.95
728 776 1.998315 CGAGAGAACCGAGTCGAGTTA 59.002 52.381 15.64 0.00 34.28 2.24
743 791 1.833860 GAGCAGGAACGAATCGAGAG 58.166 55.000 10.55 0.00 0.00 3.20
764 812 1.623542 AATCGAGAAACGGGGAGGGG 61.624 60.000 0.00 0.00 42.82 4.79
765 813 0.252197 AAATCGAGAAACGGGGAGGG 59.748 55.000 0.00 0.00 42.82 4.30
766 814 1.066430 TCAAATCGAGAAACGGGGAGG 60.066 52.381 0.00 0.00 42.82 4.30
768 816 3.343941 AATCAAATCGAGAAACGGGGA 57.656 42.857 0.00 0.00 42.82 4.81
776 839 8.128582 CCGGAAAAATATCAAATCAAATCGAGA 58.871 33.333 0.00 0.00 0.00 4.04
777 840 7.096477 GCCGGAAAAATATCAAATCAAATCGAG 60.096 37.037 5.05 0.00 0.00 4.04
885 948 6.426025 CCCCCTTGCGAAATTATTACTACTAC 59.574 42.308 0.00 0.00 0.00 2.73
886 949 6.527423 CCCCCTTGCGAAATTATTACTACTA 58.473 40.000 0.00 0.00 0.00 1.82
887 950 5.374071 CCCCCTTGCGAAATTATTACTACT 58.626 41.667 0.00 0.00 0.00 2.57
950 1013 1.266989 GAACAAACAGCTAGCACCACC 59.733 52.381 18.83 0.00 0.00 4.61
953 1016 0.881796 GGGAACAAACAGCTAGCACC 59.118 55.000 18.83 6.59 0.00 5.01
1146 1210 2.433318 AGGAGCGCGTTGAAGAGC 60.433 61.111 8.43 0.00 37.19 4.09
1173 1237 4.463879 CAGCCGTGGCAGGAGGAG 62.464 72.222 14.29 0.00 44.88 3.69
1236 1300 3.241530 ACGCTGCCCTTGTCCTCA 61.242 61.111 0.00 0.00 0.00 3.86
1269 1333 0.249868 TGTCGACCTTGCAGTCCTTG 60.250 55.000 14.12 0.00 32.91 3.61
1344 1408 0.724549 CCTCAGAGTCAGAGTCGTCG 59.275 60.000 11.22 0.00 0.00 5.12
1353 1417 1.299562 GCTCGTCGTCCTCAGAGTCA 61.300 60.000 0.00 0.00 33.57 3.41
1482 1555 1.454111 CTCCGGGTCGTCATCCTCT 60.454 63.158 0.00 0.00 0.00 3.69
1564 1637 1.053264 AGGAGCTCCTTGATGCGGAT 61.053 55.000 30.40 3.41 46.09 4.18
1636 1709 9.855021 GTTGACAAATAACAGGTTTAGCAATAT 57.145 29.630 0.00 0.00 0.00 1.28
1637 1710 9.073475 AGTTGACAAATAACAGGTTTAGCAATA 57.927 29.630 0.00 0.00 0.00 1.90
1665 1738 5.127682 TCAGATCAATGCTAAGTGCTCACTA 59.872 40.000 2.62 0.00 41.58 2.74
1703 1777 0.320683 CATCCGACTGCAAGACACCA 60.321 55.000 0.00 0.00 37.43 4.17
1862 1940 2.530701 CTCCCAATCTCGGTAGCCTAT 58.469 52.381 0.00 0.00 0.00 2.57
1871 1949 0.830648 TAACAGCCCTCCCAATCTCG 59.169 55.000 0.00 0.00 0.00 4.04
2081 2162 4.280677 ACAAAGGTAAATGGTGACCATGTG 59.719 41.667 19.32 3.40 44.40 3.21
2086 2167 3.610821 GCGAACAAAGGTAAATGGTGACC 60.611 47.826 0.00 0.00 35.83 4.02
2107 2188 4.806640 TCTCATTTTTCTTTGGGATGGC 57.193 40.909 0.00 0.00 0.00 4.40
2282 2363 9.687210 CTGATGGATGAAATAATGTAACATTGG 57.313 33.333 0.00 0.00 0.00 3.16
2325 2406 3.951680 TGCATCTGAGCATTCATTCACAT 59.048 39.130 0.00 0.00 40.11 3.21
2326 2407 3.349022 TGCATCTGAGCATTCATTCACA 58.651 40.909 0.00 0.00 40.11 3.58
2386 2467 1.059913 AGTTCCTGGGGAGTTGTCTG 58.940 55.000 0.00 0.00 31.21 3.51
2535 2616 8.886719 TCATCACTAAAACAATTCAGATAGCAG 58.113 33.333 0.00 0.00 0.00 4.24
2798 2880 6.071334 TGGTTTTGACACAGTTGAATGGTTTA 60.071 34.615 0.00 0.00 0.00 2.01
2871 2961 3.228188 TCTTGCCTTGTCAATTCTGGT 57.772 42.857 0.00 0.00 0.00 4.00
3081 3171 2.748461 TTGCAGGTTTTCTTTCGACG 57.252 45.000 0.00 0.00 0.00 5.12
3307 3495 1.001633 GCTTCCTGGTAACGTTCCTGA 59.998 52.381 2.82 5.00 42.51 3.86
3347 4323 8.962884 AAAAGAAAATATTGCAACAAAGAGGT 57.037 26.923 0.00 0.00 0.00 3.85
3375 4351 7.517320 AGGTAAACCACAAGATCATATATGCA 58.483 34.615 7.92 0.00 38.89 3.96
3478 4463 1.880027 GGTTGCCTGGTGTTACTCTTG 59.120 52.381 0.00 0.00 0.00 3.02
3556 4541 3.882888 TCAGGTGAAGGAAAACATCACAC 59.117 43.478 7.36 0.00 46.73 3.82
3768 4757 1.183549 TGACTAAACTCTCCCGAGCC 58.816 55.000 0.00 0.00 41.09 4.70
3905 4894 5.680619 TGTCCAGGATATGTGAAATGTACC 58.319 41.667 0.00 0.00 0.00 3.34
3906 4895 7.807977 AATGTCCAGGATATGTGAAATGTAC 57.192 36.000 0.00 0.00 0.00 2.90
3907 4896 8.821686 AAAATGTCCAGGATATGTGAAATGTA 57.178 30.769 0.00 0.00 0.00 2.29
3908 4897 7.722949 AAAATGTCCAGGATATGTGAAATGT 57.277 32.000 0.00 0.00 0.00 2.71
3909 4898 8.685427 TGTAAAATGTCCAGGATATGTGAAATG 58.315 33.333 0.00 0.00 0.00 2.32
3911 4900 8.685427 CATGTAAAATGTCCAGGATATGTGAAA 58.315 33.333 0.00 0.00 0.00 2.69
3912 4901 8.052141 TCATGTAAAATGTCCAGGATATGTGAA 58.948 33.333 0.00 0.00 0.00 3.18
3914 4903 7.500227 ACTCATGTAAAATGTCCAGGATATGTG 59.500 37.037 0.00 0.00 0.00 3.21
3915 4904 7.577303 ACTCATGTAAAATGTCCAGGATATGT 58.423 34.615 0.00 0.00 0.00 2.29
3920 4911 8.877864 AATAAACTCATGTAAAATGTCCAGGA 57.122 30.769 0.00 0.00 0.00 3.86
3992 4984 1.881973 CCAGCCACCGGATCATAATTG 59.118 52.381 9.46 0.00 0.00 2.32
4109 5102 1.996191 CTCTAACGAGCAGCAAGAACC 59.004 52.381 0.00 0.00 0.00 3.62
4110 5103 2.678324 ACTCTAACGAGCAGCAAGAAC 58.322 47.619 0.00 0.00 41.09 3.01
4170 5163 7.232534 AGGATAACTTAGAAATTTGCAACCACA 59.767 33.333 0.00 0.00 0.00 4.17
4303 5298 0.815213 TGCTCACGCTATTGCCCATC 60.815 55.000 0.00 0.00 36.97 3.51
4339 5334 1.212935 AGGAGGAATAAATGGTGCGCT 59.787 47.619 9.73 0.00 0.00 5.92
4357 5352 7.031975 GCAACAATGGATAAGAAGAAGAAAGG 58.968 38.462 0.00 0.00 0.00 3.11
4445 5449 1.211703 TCACAAGTCACAAGCCTTGGA 59.788 47.619 9.64 0.52 41.84 3.53
4447 5451 1.002033 GCTCACAAGTCACAAGCCTTG 60.002 52.381 2.11 2.11 42.91 3.61
4451 5455 1.571460 CGGCTCACAAGTCACAAGC 59.429 57.895 0.00 0.00 0.00 4.01
4478 5482 0.550914 AAACCAGACTGCTTGGTGGA 59.449 50.000 4.66 0.00 35.88 4.02
4479 5483 0.670162 CAAACCAGACTGCTTGGTGG 59.330 55.000 4.66 0.00 35.88 4.61
4480 5484 0.670162 CCAAACCAGACTGCTTGGTG 59.330 55.000 19.40 2.18 35.88 4.17
4481 5485 1.109323 GCCAAACCAGACTGCTTGGT 61.109 55.000 24.51 7.21 40.43 3.67
4482 5486 0.825010 AGCCAAACCAGACTGCTTGG 60.825 55.000 21.78 21.78 41.11 3.61
4483 5487 0.595095 GAGCCAAACCAGACTGCTTG 59.405 55.000 0.00 2.96 31.23 4.01
4484 5488 0.538287 GGAGCCAAACCAGACTGCTT 60.538 55.000 0.00 0.00 31.23 3.91
4522 5526 0.464452 ATAGCTGGTAACGCTGACCC 59.536 55.000 0.00 0.00 44.17 4.46


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

AutoCloner maintained by Alex Coulton.