Multiple sequence alignment - TraesCS3B01G012900

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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 TraesCS3B01G012900 chr3B 100.000 2383 0 0 1 2383 5852206 5849824 0.000000e+00 4401
1 TraesCS3B01G012900 chr3B 80.474 1055 128 38 668 1649 5773673 5772624 0.000000e+00 736
2 TraesCS3B01G012900 chr3B 83.274 562 54 22 1710 2239 5867099 5866546 4.610000e-132 481
3 TraesCS3B01G012900 chr3B 83.107 515 46 26 1762 2239 5772603 5772093 4.710000e-117 431
4 TraesCS3B01G012900 chr3B 76.123 846 134 40 650 1447 6047828 6048653 4.810000e-102 381
5 TraesCS3B01G012900 chr3B 91.321 265 21 2 1 263 6045918 6046182 6.260000e-96 361
6 TraesCS3B01G012900 chr3B 82.597 385 32 11 2021 2383 6048677 6049048 8.270000e-80 307
7 TraesCS3B01G012900 chr3B 85.926 270 21 8 295 547 6046184 6046453 3.020000e-69 272
8 TraesCS3B01G012900 chr3A 86.496 1481 146 30 585 2026 9050632 9052097 0.000000e+00 1578
9 TraesCS3B01G012900 chr3A 81.778 1136 131 39 585 1658 9007107 9008228 0.000000e+00 881
10 TraesCS3B01G012900 chr3A 85.789 380 44 8 838 1211 9010175 9010550 6.170000e-106 394
11 TraesCS3B01G012900 chr3A 85.994 357 28 11 1318 1658 8962277 8962627 1.740000e-96 363
12 TraesCS3B01G012900 chr3A 85.714 357 29 8 1318 1658 8945633 8945983 8.100000e-95 357
13 TraesCS3B01G012900 chr3A 89.680 281 25 4 1747 2026 8946045 8946322 2.910000e-94 355
14 TraesCS3B01G012900 chr3A 85.434 357 30 11 1318 1658 8979106 8979456 3.770000e-93 351
15 TraesCS3B01G012900 chr3A 79.550 533 68 20 697 1211 8948217 8948726 2.270000e-90 342
16 TraesCS3B01G012900 chr3A 83.246 382 44 11 838 1211 8981827 8982196 1.370000e-87 333
17 TraesCS3B01G012900 chr3A 82.984 382 45 11 838 1211 8964992 8965361 6.350000e-86 327
18 TraesCS3B01G012900 chr3A 87.544 281 31 3 1747 2026 8962689 8962966 2.950000e-84 322
19 TraesCS3B01G012900 chr3A 87.544 281 31 3 1747 2026 8979518 8979795 2.950000e-84 322
20 TraesCS3B01G012900 chr3A 91.266 229 15 4 123 349 9048173 9048398 8.270000e-80 307
21 TraesCS3B01G012900 chr3A 82.031 384 43 13 2021 2383 9008508 9008886 1.070000e-78 303
22 TraesCS3B01G012900 chr3A 83.143 350 35 10 1318 1649 8991799 8992142 4.980000e-77 298
23 TraesCS3B01G012900 chr3A 87.879 264 15 7 342 588 9049428 9049691 6.440000e-76 294
24 TraesCS3B01G012900 chr3A 95.109 184 8 1 1 183 9047995 9048178 3.000000e-74 289
25 TraesCS3B01G012900 chr3A 90.826 109 10 0 480 588 9006922 9007030 1.910000e-31 147
26 TraesCS3B01G012900 chrUn 100.000 445 0 0 1 445 468395660 468395216 0.000000e+00 822
27 TraesCS3B01G012900 chrUn 83.615 592 61 19 668 1224 34334054 34333464 7.550000e-145 523
28 TraesCS3B01G012900 chrUn 83.274 562 54 22 1710 2239 243149361 243148808 4.610000e-132 481
29 TraesCS3B01G012900 chrUn 83.274 562 54 22 1710 2239 243162234 243161681 4.610000e-132 481
30 TraesCS3B01G012900 chrUn 83.274 562 54 22 1710 2239 270191287 270191840 4.610000e-132 481
31 TraesCS3B01G012900 chrUn 91.321 265 21 2 1 263 428538655 428538919 6.260000e-96 361
32 TraesCS3B01G012900 chrUn 82.597 385 32 11 2021 2383 36067984 36068355 8.270000e-80 307
33 TraesCS3B01G012900 chrUn 85.926 270 21 8 295 547 428538921 428539190 3.020000e-69 272
34 TraesCS3B01G012900 chrUn 81.752 137 20 5 1315 1447 36067825 36067960 2.500000e-20 110
35 TraesCS3B01G012900 chr3D 90.991 333 22 7 846 1171 623144 622813 2.170000e-120 442
36 TraesCS3B01G012900 chr3D 78.445 733 100 34 693 1388 571216 570505 2.190000e-115 425
37 TraesCS3B01G012900 chr3D 84.456 386 37 11 2021 2383 586255 585870 2.250000e-95 359
38 TraesCS3B01G012900 chr3D 90.000 260 20 5 1762 2021 686416 686163 4.910000e-87 331
39 TraesCS3B01G012900 chr3D 84.034 357 35 6 1318 1658 686779 686429 8.220000e-85 324
40 TraesCS3B01G012900 chr3D 82.740 365 39 10 1314 1658 586909 586549 1.070000e-78 303
41 TraesCS3B01G012900 chr3D 81.013 316 35 13 655 945 587623 587308 6.630000e-56 228
42 TraesCS3B01G012900 chr1D 80.695 259 47 3 2047 2303 482827538 482827795 5.200000e-47 198
43 TraesCS3B01G012900 chr5B 79.359 281 50 5 2026 2303 701054736 701055011 8.690000e-45 191


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 TraesCS3B01G012900 chr3B 5849824 5852206 2382 True 4401.000000 4401 100.000000 1 2383 1 chr3B.!!$R1 2382
1 TraesCS3B01G012900 chr3B 5772093 5773673 1580 True 583.500000 736 81.790500 668 2239 2 chr3B.!!$R3 1571
2 TraesCS3B01G012900 chr3B 5866546 5867099 553 True 481.000000 481 83.274000 1710 2239 1 chr3B.!!$R2 529
3 TraesCS3B01G012900 chr3B 6045918 6049048 3130 False 330.250000 381 83.991750 1 2383 4 chr3B.!!$F1 2382
4 TraesCS3B01G012900 chr3A 9047995 9052097 4102 False 617.000000 1578 90.187500 1 2026 4 chr3A.!!$F6 2025
5 TraesCS3B01G012900 chr3A 9006922 9010550 3628 False 431.250000 881 85.106000 480 2383 4 chr3A.!!$F5 1903
6 TraesCS3B01G012900 chr3A 8945633 8948726 3093 False 351.333333 357 84.981333 697 2026 3 chr3A.!!$F2 1329
7 TraesCS3B01G012900 chr3A 8962277 8965361 3084 False 337.333333 363 85.507333 838 2026 3 chr3A.!!$F3 1188
8 TraesCS3B01G012900 chr3A 8979106 8982196 3090 False 335.333333 351 85.408000 838 2026 3 chr3A.!!$F4 1188
9 TraesCS3B01G012900 chrUn 34333464 34334054 590 True 523.000000 523 83.615000 668 1224 1 chrUn.!!$R1 556
10 TraesCS3B01G012900 chrUn 243148808 243149361 553 True 481.000000 481 83.274000 1710 2239 1 chrUn.!!$R2 529
11 TraesCS3B01G012900 chrUn 243161681 243162234 553 True 481.000000 481 83.274000 1710 2239 1 chrUn.!!$R3 529
12 TraesCS3B01G012900 chrUn 270191287 270191840 553 False 481.000000 481 83.274000 1710 2239 1 chrUn.!!$F1 529
13 TraesCS3B01G012900 chrUn 428538655 428539190 535 False 316.500000 361 88.623500 1 547 2 chrUn.!!$F3 546
14 TraesCS3B01G012900 chrUn 36067825 36068355 530 False 208.500000 307 82.174500 1315 2383 2 chrUn.!!$F2 1068
15 TraesCS3B01G012900 chr3D 570505 571216 711 True 425.000000 425 78.445000 693 1388 1 chr3D.!!$R1 695
16 TraesCS3B01G012900 chr3D 686163 686779 616 True 327.500000 331 87.017000 1318 2021 2 chr3D.!!$R4 703
17 TraesCS3B01G012900 chr3D 585870 587623 1753 True 296.666667 359 82.736333 655 2383 3 chr3D.!!$R3 1728

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
793 4042 0.035458 ACGACTTTGAGCTCTTGGGG 59.965 55.0 16.19 2.66 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 4994 0.403271 AGATTGCCAGTTGGAGCACT 59.597 50.0 1.45 0.0 39.1 4.4 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
28 30 2.688507 GTCGACCAAAGAGAAGCATCA 58.311 47.619 3.51 0.00 0.00 3.07
79 81 1.608590 GCGCATGGCCAGTGTAATTAT 59.391 47.619 13.05 0.00 34.80 1.28
93 96 7.358435 CCAGTGTAATTATCGTTCGATTAGCAG 60.358 40.741 12.77 0.00 0.00 4.24
215 274 3.242739 CGTTGTAGATGCCCTAACAATGC 60.243 47.826 0.00 0.00 0.00 3.56
250 309 2.290260 TGGAAATCTCGACAATGTGCCT 60.290 45.455 0.00 0.00 0.00 4.75
258 317 4.213270 TCTCGACAATGTGCCTGTAAAAAG 59.787 41.667 0.00 0.00 0.00 2.27
281 340 8.747538 AAGAAACTACAATACAAAGTCAGGTT 57.252 30.769 0.00 0.00 0.00 3.50
282 341 8.154649 AGAAACTACAATACAAAGTCAGGTTG 57.845 34.615 0.00 0.00 0.00 3.77
328 387 9.503399 TTCCTCTTCAGGTTAAGAATTACTTTC 57.497 33.333 0.00 0.00 41.28 2.62
396 1494 4.755266 ATACTACAAGGCGAAATGGACT 57.245 40.909 0.00 0.00 0.00 3.85
437 1552 6.713450 AGAAACTAAAGCCCAGTTCGAATTTA 59.287 34.615 0.00 0.16 35.19 1.40
440 1555 8.570068 AACTAAAGCCCAGTTCGAATTTAATA 57.430 30.769 0.00 0.00 30.36 0.98
515 1630 4.019174 AGCCCAGTTCGAAATTCATCAAT 58.981 39.130 0.00 0.00 0.00 2.57
517 1632 5.297776 AGCCCAGTTCGAAATTCATCAATAG 59.702 40.000 0.00 0.00 0.00 1.73
522 1637 5.760253 AGTTCGAAATTCATCAATAGCCGAT 59.240 36.000 0.00 0.00 0.00 4.18
594 3741 4.391216 CACTCTGATTGCTTTGTAGTGGAG 59.609 45.833 0.00 0.00 31.46 3.86
603 3750 2.839486 TTGTAGTGGAGGCAGAGTTG 57.161 50.000 0.00 0.00 0.00 3.16
604 3751 0.976641 TGTAGTGGAGGCAGAGTTGG 59.023 55.000 0.00 0.00 0.00 3.77
605 3752 1.267121 GTAGTGGAGGCAGAGTTGGA 58.733 55.000 0.00 0.00 0.00 3.53
610 3757 1.744741 GAGGCAGAGTTGGAGCAGC 60.745 63.158 0.00 0.00 0.00 5.25
613 3760 2.688794 GCAGAGTTGGAGCAGCAGC 61.689 63.158 0.00 0.00 42.56 5.25
617 3764 0.036952 GAGTTGGAGCAGCAGCAGTA 60.037 55.000 3.17 0.00 45.49 2.74
632 3779 7.852945 GCAGCAGCAGTAGTAGTAAATATTTTG 59.147 37.037 5.91 0.00 41.58 2.44
648 3795 3.352554 TTTTGACTGTAGCACGTACGA 57.647 42.857 24.41 0.00 33.87 3.43
674 3914 3.285215 GGCCATGCATGCCTCGAG 61.285 66.667 21.69 5.13 45.70 4.04
680 3920 1.863454 CATGCATGCCTCGAGTTCTAC 59.137 52.381 14.93 0.00 0.00 2.59
730 3979 3.580084 AGGTTCAAGCCTGCAGGA 58.420 55.556 37.21 12.97 37.50 3.86
742 3991 1.218763 CTGCAGGAGCGATTGAGATG 58.781 55.000 5.57 0.00 46.23 2.90
745 3994 0.935898 CAGGAGCGATTGAGATGCAC 59.064 55.000 0.00 0.00 0.00 4.57
748 3997 1.472201 GGAGCGATTGAGATGCACTGA 60.472 52.381 0.00 0.00 0.00 3.41
753 4002 0.994247 ATTGAGATGCACTGACCCCA 59.006 50.000 0.00 0.00 0.00 4.96
758 4007 1.637553 AGATGCACTGACCCCAAAGAT 59.362 47.619 0.00 0.00 0.00 2.40
760 4009 1.619654 TGCACTGACCCCAAAGATTG 58.380 50.000 0.00 0.00 0.00 2.67
767 4016 2.441375 TGACCCCAAAGATTGAGTGTCA 59.559 45.455 0.00 0.00 33.25 3.58
773 4022 3.436015 CCAAAGATTGAGTGTCAGCAGAG 59.564 47.826 0.00 0.00 0.00 3.35
782 4031 1.789464 GTGTCAGCAGAGACGACTTTG 59.211 52.381 1.12 1.12 41.41 2.77
792 4041 1.001406 AGACGACTTTGAGCTCTTGGG 59.999 52.381 16.19 5.25 0.00 4.12
793 4042 0.035458 ACGACTTTGAGCTCTTGGGG 59.965 55.000 16.19 2.66 0.00 4.96
794 4043 1.301677 CGACTTTGAGCTCTTGGGGC 61.302 60.000 16.19 3.93 0.00 5.80
796 4045 1.381851 CTTTGAGCTCTTGGGGCCT 59.618 57.895 16.19 0.00 0.00 5.19
797 4046 0.679321 CTTTGAGCTCTTGGGGCCTC 60.679 60.000 16.19 0.00 0.00 4.70
798 4047 2.142292 TTTGAGCTCTTGGGGCCTCC 62.142 60.000 16.19 0.72 0.00 4.30
800 4049 4.722535 AGCTCTTGGGGCCTCCGA 62.723 66.667 0.00 0.00 38.76 4.55
803 4052 1.764054 CTCTTGGGGCCTCCGATCT 60.764 63.158 0.00 0.00 38.76 2.75
804 4053 1.306997 TCTTGGGGCCTCCGATCTT 60.307 57.895 0.00 0.00 38.76 2.40
808 4057 1.839296 GGGGCCTCCGATCTTAGCT 60.839 63.158 0.84 0.00 0.00 3.32
810 4059 1.339097 GGGCCTCCGATCTTAGCTAA 58.661 55.000 5.94 5.94 0.00 3.09
811 4060 1.692519 GGGCCTCCGATCTTAGCTAAA 59.307 52.381 7.74 0.00 0.00 1.85
812 4061 2.548280 GGGCCTCCGATCTTAGCTAAAC 60.548 54.545 7.74 1.76 0.00 2.01
822 4082 6.538742 CCGATCTTAGCTAAACTTTCAATGGA 59.461 38.462 7.74 0.00 0.00 3.41
824 4084 7.492669 CGATCTTAGCTAAACTTTCAATGGAGA 59.507 37.037 7.74 0.00 0.00 3.71
842 4102 3.372206 GGAGACATCGAAGGTTGTGATTG 59.628 47.826 0.00 0.00 0.00 2.67
848 4108 3.899734 TCGAAGGTTGTGATTGCATTTG 58.100 40.909 0.00 0.00 0.00 2.32
906 4172 2.864343 ACACTTGTCGTTGCTGTTAGAC 59.136 45.455 0.00 0.00 0.00 2.59
920 4186 8.302438 GTTGCTGTTAGACTACTTAACTAGGAA 58.698 37.037 0.00 0.00 0.00 3.36
926 4192 9.447157 GTTAGACTACTTAACTAGGAAGAGTGA 57.553 37.037 12.27 2.35 0.00 3.41
928 4194 6.885918 AGACTACTTAACTAGGAAGAGTGACC 59.114 42.308 12.27 0.00 0.00 4.02
929 4195 6.550163 ACTACTTAACTAGGAAGAGTGACCA 58.450 40.000 12.27 0.00 0.00 4.02
941 4208 0.179084 AGTGACCAGACACAACCACG 60.179 55.000 0.00 0.00 42.45 4.94
949 4216 1.140816 GACACAACCACGAAGAGAGC 58.859 55.000 0.00 0.00 0.00 4.09
983 4250 1.055849 TAGAACTCAAGCTGGGCACA 58.944 50.000 0.00 0.00 0.00 4.57
1009 4284 3.554692 CGTCGACCATGAAGCGGC 61.555 66.667 10.58 0.00 0.00 6.53
1010 4285 2.125512 GTCGACCATGAAGCGGCT 60.126 61.111 3.51 0.00 0.00 5.52
1011 4286 1.741770 GTCGACCATGAAGCGGCTT 60.742 57.895 16.36 16.36 0.00 4.35
1068 4343 0.108186 TCATCCTGGTGATCGTGTGC 60.108 55.000 0.00 0.00 0.00 4.57
1155 4435 8.827677 CGGTTCTACTTCTTATATTTTGGAAGG 58.172 37.037 0.00 0.00 39.33 3.46
1162 4442 5.393866 TCTTATATTTTGGAAGGGGATGCC 58.606 41.667 0.00 0.00 0.00 4.40
1187 4467 7.012232 CCCCATTTTGACATATAATTTGTTGCC 59.988 37.037 0.00 0.00 0.00 4.52
1211 4491 0.531974 CATCAGGGCATGCATTTGGC 60.532 55.000 21.36 5.33 45.13 4.52
1322 4680 4.111053 GGAAACGGGGGAGGAGGC 62.111 72.222 0.00 0.00 0.00 4.70
1397 4761 5.946942 ACAGGTGATGTGATGACTTCTAT 57.053 39.130 0.24 0.00 41.91 1.98
1414 4778 5.186021 ACTTCTATCAAGACGTTCATCTGGT 59.814 40.000 0.00 0.00 30.44 4.00
1434 4798 1.078001 CCTCCGGCGGTTAATTGGT 60.078 57.895 27.32 0.00 0.00 3.67
1437 4801 0.903942 TCCGGCGGTTAATTGGTAGT 59.096 50.000 27.32 0.00 0.00 2.73
1550 4934 4.804139 ACATTTGTATCACGTGCTAGTAGC 59.196 41.667 15.56 15.56 42.82 3.58
1610 4994 6.245408 AGCATTCACAATGGGTTTCTTACTA 58.755 36.000 0.00 0.00 39.31 1.82
1692 5077 2.851534 GCTTGTGCGAACTGGTTATTC 58.148 47.619 0.00 0.00 0.00 1.75
1699 5084 4.873827 GTGCGAACTGGTTATTCCATAAGA 59.126 41.667 0.00 0.00 46.12 2.10
1700 5085 5.353123 GTGCGAACTGGTTATTCCATAAGAA 59.647 40.000 0.00 0.00 46.12 2.52
1725 5110 4.764679 AATGCAAATGTGTTTAGCTCGA 57.235 36.364 0.00 0.00 0.00 4.04
1732 5117 6.032460 GCAAATGTGTTTAGCTCGATTGTAAC 59.968 38.462 0.00 0.00 0.00 2.50
1743 5147 2.037902 TCGATTGTAACACCCAGCAAGA 59.962 45.455 0.00 0.00 0.00 3.02
1760 5164 3.181450 GCAAGACAGTAAGGCTATCCCAT 60.181 47.826 0.00 0.00 30.53 4.00
1770 5174 0.603975 GCTATCCCATTGACTCGGCC 60.604 60.000 0.00 0.00 0.00 6.13
1804 5227 8.140112 ACTTCTTCTGTATATCTTCTTGGTGT 57.860 34.615 0.00 0.00 0.00 4.16
1905 5336 0.685097 TGCCCACTGTAGTTGACTCC 59.315 55.000 0.00 0.00 0.00 3.85
1906 5337 0.685097 GCCCACTGTAGTTGACTCCA 59.315 55.000 0.00 0.00 0.00 3.86
1907 5338 1.071699 GCCCACTGTAGTTGACTCCAA 59.928 52.381 0.00 0.00 0.00 3.53
1911 5342 4.275936 CCCACTGTAGTTGACTCCAAAAAG 59.724 45.833 0.00 0.00 33.49 2.27
1916 5348 8.190784 CACTGTAGTTGACTCCAAAAAGAAAAT 58.809 33.333 0.00 0.00 33.49 1.82
1969 5402 9.540431 AAAATTTGAAGTTGAATTTTGTTCACG 57.460 25.926 14.09 0.00 41.40 4.35
1987 5420 5.687166 TCACGGTATAATGGACCTTCTTT 57.313 39.130 0.00 0.00 34.56 2.52
2140 5618 2.031314 TTTGCCGCCGCTAGAACA 59.969 55.556 0.00 0.00 35.36 3.18
2142 5620 1.847890 TTTGCCGCCGCTAGAACAAC 61.848 55.000 0.00 0.00 35.36 3.32
2164 5642 1.227234 CCGATGCGCCACTATCACA 60.227 57.895 4.18 0.00 0.00 3.58
2165 5643 0.809636 CCGATGCGCCACTATCACAA 60.810 55.000 4.18 0.00 0.00 3.33
2182 5660 4.160329 TCACAACTCCCATACTGAAGTCT 58.840 43.478 0.00 0.00 0.00 3.24
2185 5663 5.186021 CACAACTCCCATACTGAAGTCTACT 59.814 44.000 0.00 0.00 0.00 2.57
2200 5678 7.652727 TGAAGTCTACTTGATCTTATCGATGG 58.347 38.462 8.54 0.78 36.11 3.51
2201 5679 7.502561 TGAAGTCTACTTGATCTTATCGATGGA 59.497 37.037 8.54 6.77 36.11 3.41
2208 5686 5.109662 TGATCTTATCGATGGAAGTCGTC 57.890 43.478 8.54 6.10 42.07 4.20
2216 5694 3.005472 TCGATGGAAGTCGTCAAGTCTTT 59.995 43.478 0.00 0.00 42.07 2.52
2258 5736 4.025858 GCCCCAGAGCTGCAGTCA 62.026 66.667 16.64 0.00 0.00 3.41
2274 5752 2.096496 CAGTCATTGGCGTTGAATCCTC 59.904 50.000 0.00 0.00 0.00 3.71
2298 5777 5.004821 CGAATTGATCTGAAGAACCTACACG 59.995 44.000 0.00 0.00 0.00 4.49
2329 5828 4.602259 GTATAGCCTGCCGCGCCA 62.602 66.667 0.00 0.00 44.76 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.069273 CTTCTCTTTGGTCGACGCATT 58.931 47.619 9.92 0.00 0.00 3.56
79 81 1.876714 GCCGCTGCTAATCGAACGA 60.877 57.895 0.00 0.00 33.53 3.85
93 96 3.849953 CAAGACGCTAACCGCCGC 61.850 66.667 0.00 0.00 41.76 6.53
98 101 0.321298 TCCAAGGCAAGACGCTAACC 60.321 55.000 0.00 0.00 41.91 2.85
112 115 0.035458 AAGCGACCAGGTCTTCCAAG 59.965 55.000 17.95 1.80 35.89 3.61
159 162 5.304871 TGACTAGTCGCTTATAGAGGAGAGA 59.695 44.000 17.85 0.00 0.00 3.10
215 274 1.164411 TTTCCAAGCCGTGCATGTAG 58.836 50.000 4.96 0.00 0.00 2.74
258 317 8.149973 TCAACCTGACTTTGTATTGTAGTTTC 57.850 34.615 0.00 0.00 0.00 2.78
276 335 6.118170 ACATAGTCTTGGATGAATCAACCTG 58.882 40.000 10.89 4.33 0.00 4.00
278 337 7.396540 AAACATAGTCTTGGATGAATCAACC 57.603 36.000 2.26 2.26 0.00 3.77
281 340 7.405292 AGGAAAACATAGTCTTGGATGAATCA 58.595 34.615 0.00 0.00 0.00 2.57
282 341 7.772757 AGAGGAAAACATAGTCTTGGATGAATC 59.227 37.037 0.00 0.00 0.00 2.52
328 387 7.988737 TGATTGATGCATAACCTTGTCTAAAG 58.011 34.615 0.00 0.00 0.00 1.85
410 1509 2.742589 CGAACTGGGCTTTAGTTTCTCC 59.257 50.000 0.00 0.00 38.42 3.71
440 1555 6.070824 GGGTTGTTCAGTCCATTTCCATATTT 60.071 38.462 0.00 0.00 0.00 1.40
515 1630 5.337571 CCTGGCTCTGATAAATTATCGGCTA 60.338 44.000 15.19 11.92 40.58 3.93
517 1632 3.686726 CCTGGCTCTGATAAATTATCGGC 59.313 47.826 15.19 14.01 40.58 5.54
522 1637 5.984725 TCGAAACCTGGCTCTGATAAATTA 58.015 37.500 0.00 0.00 0.00 1.40
594 3741 2.033141 TGCTGCTCCAACTCTGCC 59.967 61.111 0.00 0.00 0.00 4.85
603 3750 0.820871 ACTACTACTGCTGCTGCTCC 59.179 55.000 17.00 0.00 40.48 4.70
604 3751 3.784701 TTACTACTACTGCTGCTGCTC 57.215 47.619 17.00 0.00 40.48 4.26
605 3752 4.744795 ATTTACTACTACTGCTGCTGCT 57.255 40.909 17.00 0.00 40.48 4.24
617 3764 9.084164 CGTGCTACAGTCAAAATATTTACTACT 57.916 33.333 0.01 3.04 0.00 2.57
632 3779 2.608467 AACTCGTACGTGCTACAGTC 57.392 50.000 16.05 0.00 0.00 3.51
639 3786 1.463528 GCCATCAAAACTCGTACGTGC 60.464 52.381 16.05 0.00 0.00 5.34
648 3795 1.406341 GCATGCATGGCCATCAAAACT 60.406 47.619 27.34 0.00 0.00 2.66
674 3914 4.274950 TGGCAAGTGCAAGTAAAGTAGAAC 59.725 41.667 5.52 0.00 44.36 3.01
680 3920 1.337703 TGCTGGCAAGTGCAAGTAAAG 59.662 47.619 9.40 0.00 43.95 1.85
713 3954 1.377994 CTCCTGCAGGCTTGAACCT 59.622 57.895 28.91 0.00 42.30 3.50
728 3977 0.935898 CAGTGCATCTCAATCGCTCC 59.064 55.000 0.00 0.00 0.00 4.70
729 3978 1.592081 GTCAGTGCATCTCAATCGCTC 59.408 52.381 0.00 0.00 0.00 5.03
730 3979 1.649664 GTCAGTGCATCTCAATCGCT 58.350 50.000 0.00 0.00 0.00 4.93
742 3991 1.815003 CTCAATCTTTGGGGTCAGTGC 59.185 52.381 0.00 0.00 0.00 4.40
745 3994 3.077359 GACACTCAATCTTTGGGGTCAG 58.923 50.000 0.00 0.00 35.60 3.51
748 3997 2.815589 GCTGACACTCAATCTTTGGGGT 60.816 50.000 0.00 0.00 34.70 4.95
753 4002 4.314121 GTCTCTGCTGACACTCAATCTTT 58.686 43.478 0.00 0.00 36.97 2.52
758 4007 1.001268 GTCGTCTCTGCTGACACTCAA 60.001 52.381 0.00 0.00 36.82 3.02
760 4009 0.878416 AGTCGTCTCTGCTGACACTC 59.122 55.000 0.00 0.00 36.82 3.51
767 4016 0.965439 AGCTCAAAGTCGTCTCTGCT 59.035 50.000 0.00 0.00 0.00 4.24
773 4022 1.433534 CCCAAGAGCTCAAAGTCGTC 58.566 55.000 17.77 0.00 0.00 4.20
782 4031 4.168291 CGGAGGCCCCAAGAGCTC 62.168 72.222 5.27 5.27 34.14 4.09
792 4041 2.365941 AGTTTAGCTAAGATCGGAGGCC 59.634 50.000 6.24 0.00 0.00 5.19
793 4042 3.737032 AGTTTAGCTAAGATCGGAGGC 57.263 47.619 6.24 0.00 0.00 4.70
794 4043 5.661458 TGAAAGTTTAGCTAAGATCGGAGG 58.339 41.667 6.24 0.00 0.00 4.30
796 4045 6.538742 CCATTGAAAGTTTAGCTAAGATCGGA 59.461 38.462 6.24 0.00 0.00 4.55
797 4046 6.538742 TCCATTGAAAGTTTAGCTAAGATCGG 59.461 38.462 6.24 0.33 0.00 4.18
798 4047 7.492669 TCTCCATTGAAAGTTTAGCTAAGATCG 59.507 37.037 6.24 0.00 0.00 3.69
800 4049 8.103305 TGTCTCCATTGAAAGTTTAGCTAAGAT 58.897 33.333 6.24 0.00 0.00 2.40
803 4052 7.064609 CGATGTCTCCATTGAAAGTTTAGCTAA 59.935 37.037 0.86 0.86 34.81 3.09
804 4053 6.535150 CGATGTCTCCATTGAAAGTTTAGCTA 59.465 38.462 0.00 0.00 34.81 3.32
808 4057 6.371548 CCTTCGATGTCTCCATTGAAAGTTTA 59.628 38.462 6.77 0.00 46.18 2.01
810 4059 4.697352 CCTTCGATGTCTCCATTGAAAGTT 59.303 41.667 6.77 0.00 46.18 2.66
811 4060 4.256920 CCTTCGATGTCTCCATTGAAAGT 58.743 43.478 6.77 0.00 46.18 2.66
812 4061 4.256920 ACCTTCGATGTCTCCATTGAAAG 58.743 43.478 6.77 4.07 46.18 2.62
822 4082 2.744202 GCAATCACAACCTTCGATGTCT 59.256 45.455 0.00 0.00 0.00 3.41
824 4084 2.503331 TGCAATCACAACCTTCGATGT 58.497 42.857 0.00 0.00 0.00 3.06
827 4087 3.305267 CCAAATGCAATCACAACCTTCGA 60.305 43.478 0.00 0.00 0.00 3.71
828 4088 2.988493 CCAAATGCAATCACAACCTTCG 59.012 45.455 0.00 0.00 0.00 3.79
842 4102 7.315142 TCTGAACATCTTGATTAACCAAATGC 58.685 34.615 5.24 0.00 0.00 3.56
848 4108 8.729805 AGATTCTCTGAACATCTTGATTAACC 57.270 34.615 0.00 0.00 0.00 2.85
906 4172 6.885376 TCTGGTCACTCTTCCTAGTTAAGTAG 59.115 42.308 9.99 9.99 0.00 2.57
920 4186 1.139058 GTGGTTGTGTCTGGTCACTCT 59.861 52.381 0.00 0.00 38.90 3.24
926 4192 0.828022 TCTTCGTGGTTGTGTCTGGT 59.172 50.000 0.00 0.00 0.00 4.00
928 4194 2.398498 CTCTCTTCGTGGTTGTGTCTG 58.602 52.381 0.00 0.00 0.00 3.51
929 4195 1.269831 GCTCTCTTCGTGGTTGTGTCT 60.270 52.381 0.00 0.00 0.00 3.41
962 4229 1.807142 GTGCCCAGCTTGAGTTCTAAC 59.193 52.381 0.00 0.00 0.00 2.34
971 4238 0.535780 TCTTGTCTGTGCCCAGCTTG 60.536 55.000 0.00 0.00 38.66 4.01
983 4250 2.092323 TCATGGTCGACGATCTTGTCT 58.908 47.619 19.77 0.00 36.71 3.41
986 4253 1.590238 GCTTCATGGTCGACGATCTTG 59.410 52.381 15.80 15.80 0.00 3.02
989 4256 1.209275 CCGCTTCATGGTCGACGATC 61.209 60.000 10.39 0.00 0.00 3.69
991 4258 2.180769 CCGCTTCATGGTCGACGA 59.819 61.111 9.92 5.99 0.00 4.20
992 4259 3.554692 GCCGCTTCATGGTCGACG 61.555 66.667 9.92 0.00 0.00 5.12
993 4260 1.298859 AAAGCCGCTTCATGGTCGAC 61.299 55.000 7.13 7.13 0.00 4.20
1042 4317 3.070159 ACGATCACCAGGATGATTACCAG 59.930 47.826 0.00 0.00 39.48 4.00
1046 4321 3.741075 GCACACGATCACCAGGATGATTA 60.741 47.826 0.00 0.00 39.48 1.75
1126 4406 8.533657 TCCAAAATATAAGAAGTAGAACCGACA 58.466 33.333 0.00 0.00 0.00 4.35
1137 4417 6.015095 GGCATCCCCTTCCAAAATATAAGAAG 60.015 42.308 0.00 0.00 36.35 2.85
1162 4442 7.918643 GGCAACAAATTATATGTCAAAATGGG 58.081 34.615 0.00 0.00 0.00 4.00
1187 4467 1.471829 ATGCATGCCCTGATGCCATG 61.472 55.000 16.68 0.00 46.98 3.66
1201 4481 0.968405 ACCAAAGTCGCCAAATGCAT 59.032 45.000 0.00 0.00 41.33 3.96
1211 4491 1.373497 AGCGCTCTGACCAAAGTCG 60.373 57.895 2.64 0.00 46.74 4.18
1255 4548 0.688749 AGCCCCCTGATCAAATTGGC 60.689 55.000 14.26 14.26 37.68 4.52
1322 4680 1.012486 GCGTCCGTCCTACTTGGTTG 61.012 60.000 0.00 0.00 37.07 3.77
1393 4753 4.678044 GCACCAGATGAACGTCTTGATAGA 60.678 45.833 0.00 0.00 0.00 1.98
1396 4760 2.350522 GCACCAGATGAACGTCTTGAT 58.649 47.619 0.00 0.00 0.00 2.57
1397 4761 1.608025 GGCACCAGATGAACGTCTTGA 60.608 52.381 0.00 0.00 0.00 3.02
1434 4798 3.355378 CCAAACCATCAGCCATCAACTA 58.645 45.455 0.00 0.00 0.00 2.24
1437 4801 1.076841 TCCCAAACCATCAGCCATCAA 59.923 47.619 0.00 0.00 0.00 2.57
1570 4954 2.871182 TGCTCGCTCTCGAATAACAT 57.129 45.000 0.00 0.00 44.98 2.71
1575 4959 1.134995 TGTGAATGCTCGCTCTCGAAT 60.135 47.619 0.00 0.00 44.98 3.34
1610 4994 0.403271 AGATTGCCAGTTGGAGCACT 59.597 50.000 1.45 0.00 39.10 4.40
1699 5084 7.812191 TCGAGCTAAACACATTTGCATTAATTT 59.188 29.630 0.00 0.00 0.00 1.82
1700 5085 7.312154 TCGAGCTAAACACATTTGCATTAATT 58.688 30.769 0.00 0.00 0.00 1.40
1714 5099 3.998341 GGGTGTTACAATCGAGCTAAACA 59.002 43.478 0.00 0.00 0.00 2.83
1725 5110 3.149196 CTGTCTTGCTGGGTGTTACAAT 58.851 45.455 0.00 0.00 0.00 2.71
1732 5117 1.813513 CCTTACTGTCTTGCTGGGTG 58.186 55.000 0.00 0.00 0.00 4.61
1743 5147 4.040755 AGTCAATGGGATAGCCTTACTGT 58.959 43.478 0.00 0.00 0.00 3.55
1760 5164 3.241530 ACTGGCTGGCCGAGTCAA 61.242 61.111 10.14 0.00 35.27 3.18
1770 5174 2.540265 ACAGAAGAAGTCACTGGCTG 57.460 50.000 0.00 0.00 36.17 4.85
1804 5227 4.145807 GGATCAGTAGAAAGGAGATCGGA 58.854 47.826 0.00 0.00 36.76 4.55
1891 5322 7.696992 TTTTCTTTTTGGAGTCAACTACAGT 57.303 32.000 0.00 0.00 38.22 3.55
1987 5420 2.884146 GCACGCTGACATGCAAAAA 58.116 47.368 0.00 0.00 41.65 1.94
2098 5566 3.716195 CGGTGGTCCATGGCCTCA 61.716 66.667 21.23 10.94 0.00 3.86
2099 5567 2.966732 TTCGGTGGTCCATGGCCTC 61.967 63.158 21.23 18.07 0.00 4.70
2102 5573 3.124921 CGTTCGGTGGTCCATGGC 61.125 66.667 6.96 1.78 0.00 4.40
2134 5605 1.448893 GCATCGGCGGGTTGTTCTA 60.449 57.895 7.21 0.00 0.00 2.10
2164 5642 6.017192 TCAAGTAGACTTCAGTATGGGAGTT 58.983 40.000 0.00 0.00 34.04 3.01
2165 5643 5.580998 TCAAGTAGACTTCAGTATGGGAGT 58.419 41.667 0.00 0.00 36.01 3.85
2182 5660 6.262496 ACGACTTCCATCGATAAGATCAAGTA 59.738 38.462 13.60 0.00 45.13 2.24
2185 5663 5.067283 TGACGACTTCCATCGATAAGATCAA 59.933 40.000 13.60 0.00 45.13 2.57
2200 5678 2.607635 TGCACAAAGACTTGACGACTTC 59.392 45.455 0.00 0.00 36.33 3.01
2201 5679 2.351726 GTGCACAAAGACTTGACGACTT 59.648 45.455 13.17 0.00 36.33 3.01
2208 5686 0.592247 GGCACGTGCACAAAGACTTG 60.592 55.000 38.60 0.00 44.36 3.16
2251 5729 1.199789 GATTCAACGCCAATGACTGCA 59.800 47.619 0.00 0.00 0.00 4.41
2258 5736 2.107950 TTCGAGGATTCAACGCCAAT 57.892 45.000 0.00 0.00 0.00 3.16
2274 5752 5.004821 CGTGTAGGTTCTTCAGATCAATTCG 59.995 44.000 0.00 0.00 0.00 3.34
2298 5777 4.034048 CAGGCTATACAACGGTGTGATTTC 59.966 45.833 18.38 3.10 38.82 2.17
2329 5828 2.573462 TGTAGATTCTTGCCAGCTCCTT 59.427 45.455 0.00 0.00 0.00 3.36
2341 5840 5.815581 AGATAGAGCTCCGATGTAGATTCT 58.184 41.667 10.93 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.