Multiple sequence alignment - TraesCS5A01G402600

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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 TraesCS5A01G402600 chr5A 100.000 2542 0 0 1 2542 595370952 595373493 0.000000e+00 4695.0
1 TraesCS5A01G402600 chr5A 87.391 230 29 0 319 548 232475126 232474897 5.390000e-67 265.0
2 TraesCS5A01G402600 chr5D 88.548 1563 88 48 169 1692 475836663 475838173 0.000000e+00 1810.0
3 TraesCS5A01G402600 chr5D 87.614 549 48 11 2002 2539 475838651 475839190 9.990000e-174 619.0
4 TraesCS5A01G402600 chr5B 93.843 1007 35 13 691 1693 583202787 583203770 0.000000e+00 1491.0
5 TraesCS5A01G402600 chr5B 88.725 541 53 6 2002 2539 583204247 583204782 0.000000e+00 654.0
6 TraesCS5A01G402600 chr5B 93.365 211 14 0 336 546 583201707 583201917 1.900000e-81 313.0
7 TraesCS5A01G402600 chr5B 93.478 138 8 1 1 138 583199797 583199933 1.190000e-48 204.0
8 TraesCS5A01G402600 chr5B 90.132 152 4 7 550 697 583202340 583202484 1.200000e-43 187.0
9 TraesCS5A01G402600 chr5B 91.150 113 6 4 1864 1974 583204068 583204178 1.580000e-32 150.0
10 TraesCS5A01G402600 chr7A 90.278 288 25 3 1 287 694038261 694038546 8.590000e-100 374.0
11 TraesCS5A01G402600 chr7A 88.750 240 27 0 309 548 694038541 694038780 6.880000e-76 294.0
12 TraesCS5A01G402600 chr7A 87.903 248 30 0 301 548 564349160 564349407 2.470000e-75 292.0
13 TraesCS5A01G402600 chr7A 91.573 178 12 3 1 177 564348416 564348591 2.530000e-60 243.0
14 TraesCS5A01G402600 chr7A 85.950 121 15 1 167 287 564349055 564349173 7.380000e-26 128.0
15 TraesCS5A01G402600 chr4D 88.256 281 32 1 7 287 397672755 397672476 4.050000e-88 335.0
16 TraesCS5A01G402600 chr4D 90.909 242 22 0 307 548 397672483 397672242 2.440000e-85 326.0
17 TraesCS5A01G402600 chr4D 86.697 218 27 2 301 518 411559861 411559646 9.090000e-60 241.0
18 TraesCS5A01G402600 chr2D 88.889 243 27 0 301 543 545008391 545008149 1.480000e-77 300.0
19 TraesCS5A01G402600 chr3D 92.857 70 0 3 561 628 554348433 554348367 2.080000e-16 97.1
20 TraesCS5A01G402600 chr6D 88.750 80 5 2 549 627 453318656 453318732 7.490000e-16 95.3
21 TraesCS5A01G402600 chr6D 86.047 86 7 4 549 632 301047633 301047715 1.250000e-13 87.9


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 TraesCS5A01G402600 chr5A 595370952 595373493 2541 False 4695.000000 4695 100.000000 1 2542 1 chr5A.!!$F1 2541
1 TraesCS5A01G402600 chr5D 475836663 475839190 2527 False 1214.500000 1810 88.081000 169 2539 2 chr5D.!!$F1 2370
2 TraesCS5A01G402600 chr5B 583199797 583204782 4985 False 499.833333 1491 91.782167 1 2539 6 chr5B.!!$F1 2538
3 TraesCS5A01G402600 chr7A 694038261 694038780 519 False 334.000000 374 89.514000 1 548 2 chr7A.!!$F2 547
4 TraesCS5A01G402600 chr7A 564348416 564349407 991 False 221.000000 292 88.475333 1 548 3 chr7A.!!$F1 547
5 TraesCS5A01G402600 chr4D 397672242 397672755 513 True 330.500000 335 89.582500 7 548 2 chr4D.!!$R2 541

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
235 2393 0.321671 AGGGATGAACACGGTCACTG 59.678 55.0 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 5419 1.065251 GAATGCTGCTTAGAGCCTTGC 59.935 52.381 0.0 0.89 41.51 4.01 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 29 0.611714 GACCAATGTCTACCCACCGT 59.388 55.000 0.00 0.00 38.53 4.83
34 35 2.243602 TGTCTACCCACCGTTTTGTC 57.756 50.000 0.00 0.00 0.00 3.18
95 96 1.671742 GACTTCCACTTCGGCAGGA 59.328 57.895 0.00 0.00 31.16 3.86
117 118 4.320023 ACGTGCACTTGTAATACCAATGA 58.680 39.130 16.19 0.00 0.00 2.57
172 2330 6.990349 CACGTTAAAATCTATGTAGATGGGGT 59.010 38.462 3.44 0.00 41.96 4.95
180 2338 4.785914 TCTATGTAGATGGGGTTTTGTCCA 59.214 41.667 0.00 0.00 37.46 4.02
235 2393 0.321671 AGGGATGAACACGGTCACTG 59.678 55.000 0.00 0.00 0.00 3.66
259 2417 3.085952 TGGGTCCTCATCAATTGTTCC 57.914 47.619 5.13 0.00 0.00 3.62
283 2441 3.198417 CCCGGTGTTATTAACCCTACAGT 59.802 47.826 0.00 0.00 33.88 3.55
284 2442 4.323715 CCCGGTGTTATTAACCCTACAGTT 60.324 45.833 0.00 0.00 33.88 3.16
285 2443 5.247862 CCGGTGTTATTAACCCTACAGTTT 58.752 41.667 4.17 0.00 33.88 2.66
286 2444 5.706833 CCGGTGTTATTAACCCTACAGTTTT 59.293 40.000 4.17 0.00 33.88 2.43
287 2445 6.207221 CCGGTGTTATTAACCCTACAGTTTTT 59.793 38.462 4.17 0.00 33.88 1.94
329 2487 5.133221 ACAGTTTTAGAGACCATTGCTTGT 58.867 37.500 0.00 0.00 0.00 3.16
391 2549 8.144478 GGATCACTTGATAATTGCTAGTGTCTA 58.856 37.037 17.35 6.13 39.20 2.59
515 2673 1.929230 TGTTCGAAAGTCGTGCTTCA 58.071 45.000 0.00 0.00 41.35 3.02
519 2677 3.519908 TCGAAAGTCGTGCTTCAAATG 57.480 42.857 0.00 0.00 41.35 2.32
603 3180 9.320295 TCCCTTTGAATATTGTTCCAAATTACT 57.680 29.630 0.00 0.00 0.00 2.24
680 3260 1.201647 TGGATTCCACGAACGACTCTC 59.798 52.381 0.00 0.00 0.00 3.20
681 3261 1.536149 GATTCCACGAACGACTCTCG 58.464 55.000 0.14 0.00 46.93 4.04
854 3743 0.607217 CCCCCGTACAAAACCACTCC 60.607 60.000 0.00 0.00 0.00 3.85
855 3744 0.399075 CCCCGTACAAAACCACTCCT 59.601 55.000 0.00 0.00 0.00 3.69
856 3745 1.202842 CCCCGTACAAAACCACTCCTT 60.203 52.381 0.00 0.00 0.00 3.36
857 3746 2.148768 CCCGTACAAAACCACTCCTTC 58.851 52.381 0.00 0.00 0.00 3.46
919 3808 2.363172 GCCACACTCCCTCCTCCTC 61.363 68.421 0.00 0.00 0.00 3.71
920 3809 1.687493 CCACACTCCCTCCTCCTCC 60.687 68.421 0.00 0.00 0.00 4.30
921 3810 1.390125 CACACTCCCTCCTCCTCCT 59.610 63.158 0.00 0.00 0.00 3.69
922 3811 0.686112 CACACTCCCTCCTCCTCCTC 60.686 65.000 0.00 0.00 0.00 3.71
956 3857 3.058224 CCAAGAACTCCAAAAGGTAAGCG 60.058 47.826 0.00 0.00 0.00 4.68
963 3864 3.343617 TCCAAAAGGTAAGCGATCCAAG 58.656 45.455 0.00 0.00 0.00 3.61
966 3867 0.462047 AAGGTAAGCGATCCAAGCCG 60.462 55.000 0.00 0.00 34.64 5.52
985 3887 1.222115 GCATTCCCGTACCAGATCGC 61.222 60.000 0.00 0.00 0.00 4.58
994 3896 4.519437 CCAGATCGCAGCTCGCCA 62.519 66.667 3.09 0.00 37.30 5.69
1000 3902 3.869272 CGCAGCTCGCCACCAATC 61.869 66.667 3.09 0.00 37.30 2.67
1001 3903 2.747460 GCAGCTCGCCACCAATCA 60.747 61.111 0.00 0.00 32.94 2.57
1002 3904 2.758089 GCAGCTCGCCACCAATCAG 61.758 63.158 0.00 0.00 32.94 2.90
1018 3920 1.186200 TCAGCTGCGGATTACTCAGT 58.814 50.000 9.47 0.00 0.00 3.41
1026 3928 2.678190 GCGGATTACTCAGTCCTTGCTT 60.678 50.000 0.00 0.00 32.19 3.91
1143 4045 2.881352 GCGGCGAAGAAGAGGTCG 60.881 66.667 12.98 0.00 40.24 4.79
1444 4346 1.029681 GTGAGTGAAACCCAACCCAC 58.970 55.000 0.00 0.00 37.80 4.61
1480 4382 0.878523 TGACCAGCCGTTTCAGTTCG 60.879 55.000 0.00 0.00 0.00 3.95
1637 4544 4.161333 CCTGCAAATTTGTCTCGATTGTC 58.839 43.478 19.03 0.00 0.00 3.18
1648 4555 1.807981 CGATTGTCCGCCGCTTGTA 60.808 57.895 0.00 0.00 0.00 2.41
1663 4570 5.508153 GCCGCTTGTATGATTCTTCTCTAGA 60.508 44.000 0.00 0.00 0.00 2.43
1693 4600 4.642885 ACACTTCGAAAGGGAAAATGTTCA 59.357 37.500 0.00 0.00 35.35 3.18
1695 4602 6.488683 ACACTTCGAAAGGGAAAATGTTCATA 59.511 34.615 0.00 0.00 35.35 2.15
1703 4661 8.525290 AAAGGGAAAATGTTCATAGGTCATAG 57.475 34.615 0.00 0.00 35.25 2.23
1708 4666 6.683974 AAATGTTCATAGGTCATAGTGCAC 57.316 37.500 9.40 9.40 0.00 4.57
1721 4679 5.411361 GTCATAGTGCACCATTGTCTAACAA 59.589 40.000 14.63 0.00 42.95 2.83
1725 4683 4.644685 AGTGCACCATTGTCTAACAACTTT 59.355 37.500 14.63 0.00 41.40 2.66
1736 4694 5.588648 TGTCTAACAACTTTCAGACCCAAAG 59.411 40.000 0.00 0.00 37.25 2.77
1737 4695 5.589050 GTCTAACAACTTTCAGACCCAAAGT 59.411 40.000 0.00 0.00 44.34 2.66
1738 4696 4.983671 AACAACTTTCAGACCCAAAGTC 57.016 40.909 0.00 0.00 42.14 3.01
1754 4796 6.214819 ACCCAAAGTCATACATACTTGGTAGT 59.785 38.462 0.00 0.00 37.26 2.73
1761 4803 7.837689 AGTCATACATACTTGGTAGTAAGGTGA 59.162 37.037 0.00 0.00 40.14 4.02
1767 4809 8.258708 ACATACTTGGTAGTAAGGTGAGAAATC 58.741 37.037 0.00 0.00 40.14 2.17
1768 4810 6.936968 ACTTGGTAGTAAGGTGAGAAATCT 57.063 37.500 0.00 0.00 31.21 2.40
1770 4812 6.497259 ACTTGGTAGTAAGGTGAGAAATCTGA 59.503 38.462 0.00 0.00 31.21 3.27
1783 4825 7.126398 GTGAGAAATCTGAAACAACAGTGTAC 58.874 38.462 0.00 0.00 36.80 2.90
1789 4831 6.222038 TCTGAAACAACAGTGTACTCTCTT 57.778 37.500 0.00 0.00 36.80 2.85
1790 4832 6.273825 TCTGAAACAACAGTGTACTCTCTTC 58.726 40.000 0.00 0.00 36.80 2.87
1791 4833 5.972935 TGAAACAACAGTGTACTCTCTTCA 58.027 37.500 0.00 0.00 36.80 3.02
1792 4834 6.042777 TGAAACAACAGTGTACTCTCTTCAG 58.957 40.000 0.00 0.00 36.80 3.02
1793 4835 4.592485 ACAACAGTGTACTCTCTTCAGG 57.408 45.455 0.00 0.00 35.72 3.86
1794 4836 3.243907 ACAACAGTGTACTCTCTTCAGGC 60.244 47.826 0.00 0.00 35.72 4.85
1795 4837 2.883026 ACAGTGTACTCTCTTCAGGCT 58.117 47.619 0.00 0.00 0.00 4.58
1804 4857 4.357325 ACTCTCTTCAGGCTTGGAGAATA 58.643 43.478 8.37 0.00 38.49 1.75
1805 4858 4.780021 ACTCTCTTCAGGCTTGGAGAATAA 59.220 41.667 8.37 0.00 38.49 1.40
1811 4864 5.755409 TCAGGCTTGGAGAATAACTACAA 57.245 39.130 0.00 0.00 46.01 2.41
1845 4958 2.091541 GGGGCATTCGATTCACAAGAA 58.908 47.619 0.00 0.00 38.31 2.52
1863 4976 4.255510 AGAATATGCCCATGTTGACCTT 57.744 40.909 0.00 0.00 0.00 3.50
1865 4978 5.380043 AGAATATGCCCATGTTGACCTTAG 58.620 41.667 0.00 0.00 0.00 2.18
1872 4985 5.007682 GCCCATGTTGACCTTAGTTTCTTA 58.992 41.667 0.00 0.00 0.00 2.10
1874 4987 6.472887 CCCATGTTGACCTTAGTTTCTTAGA 58.527 40.000 0.00 0.00 0.00 2.10
1875 4988 6.940298 CCCATGTTGACCTTAGTTTCTTAGAA 59.060 38.462 0.00 0.00 0.00 2.10
1918 5075 4.098654 TCGAAAGGGAAAATGTTCTGCAAA 59.901 37.500 0.00 0.00 33.92 3.68
1954 5111 6.822667 ACATTCAGAAGTCATAATGCAACA 57.177 33.333 0.00 0.00 33.57 3.33
1968 5125 5.717078 AATGCAACATTGTCTGACATCTT 57.283 34.783 11.86 0.66 0.00 2.40
1969 5126 4.754372 TGCAACATTGTCTGACATCTTC 57.246 40.909 11.86 0.56 0.00 2.87
1970 5127 3.503363 TGCAACATTGTCTGACATCTTCC 59.497 43.478 11.86 0.29 0.00 3.46
1980 5171 2.663602 CTGACATCTTCCTGAAACGACG 59.336 50.000 0.00 0.00 0.00 5.12
1997 5188 4.545610 ACGACGGTGTATTTTCTCGTAAA 58.454 39.130 0.00 0.00 32.84 2.01
1998 5189 5.163513 ACGACGGTGTATTTTCTCGTAAAT 58.836 37.500 0.00 0.00 32.84 1.40
1999 5190 5.287035 ACGACGGTGTATTTTCTCGTAAATC 59.713 40.000 0.00 0.00 32.84 2.17
2000 5191 5.514204 CGACGGTGTATTTTCTCGTAAATCT 59.486 40.000 0.00 0.00 34.06 2.40
2025 5225 0.898320 TGTCCTGGCTTCAGACTAGC 59.102 55.000 0.00 0.00 40.86 3.42
2068 5268 6.722301 CAGAATATGCAATACACAGAACAGG 58.278 40.000 0.00 0.00 0.00 4.00
2069 5269 5.824624 AGAATATGCAATACACAGAACAGGG 59.175 40.000 0.00 0.00 0.00 4.45
2070 5270 3.719268 ATGCAATACACAGAACAGGGA 57.281 42.857 0.00 0.00 0.00 4.20
2121 5321 2.838736 ACAAGAGCACCTGTTACAGTG 58.161 47.619 11.68 10.38 0.00 3.66
2156 5362 4.831107 TCATGTGTTTCTGCACTATAGCA 58.169 39.130 0.00 0.00 43.35 3.49
2180 5387 7.352739 CAGACAAATAAGTAAAACGTTCTGCT 58.647 34.615 0.00 0.00 0.00 4.24
2182 5389 9.048446 AGACAAATAAGTAAAACGTTCTGCTAA 57.952 29.630 0.00 0.00 0.00 3.09
2183 5390 9.654417 GACAAATAAGTAAAACGTTCTGCTAAA 57.346 29.630 0.00 0.00 0.00 1.85
2264 5471 4.932200 CCCAAGTACAACAAGAGACATCTC 59.068 45.833 0.26 0.26 43.17 2.75
2306 5513 2.557920 AGCTAGCAGTGCTTTGTTCT 57.442 45.000 25.23 10.33 40.44 3.01
2318 5525 6.919662 CAGTGCTTTGTTCTGTTGATTACATT 59.080 34.615 0.00 0.00 35.85 2.71
2327 5534 3.355378 TGTTGATTACATTGGCCTCTGG 58.645 45.455 3.32 0.00 0.00 3.86
2369 5576 2.223665 GCTGATGAAAGCCATAACCAGC 60.224 50.000 0.00 0.00 37.20 4.85
2380 5587 2.482142 CCATAACCAGCGAGGAGAAGAC 60.482 54.545 5.19 0.00 41.22 3.01
2426 5633 0.179000 GCCACTCCAATGATCTCCGT 59.821 55.000 0.00 0.00 0.00 4.69
2438 5645 4.371855 TGATCTCCGTAAGTAACTGCAG 57.628 45.455 13.48 13.48 0.00 4.41
2439 5646 2.649331 TCTCCGTAAGTAACTGCAGC 57.351 50.000 15.27 0.00 0.00 5.25
2442 5649 2.860735 CTCCGTAAGTAACTGCAGCATC 59.139 50.000 15.27 3.97 0.00 3.91
2447 5654 3.813529 AAGTAACTGCAGCATCGTTTC 57.186 42.857 15.27 0.00 0.00 2.78
2471 5678 3.228749 CATGTTTAGCAGCGTGAACAAG 58.771 45.455 13.01 7.18 35.83 3.16
2476 5683 1.882912 AGCAGCGTGAACAAGAATGA 58.117 45.000 0.00 0.00 0.00 2.57
2478 5685 2.031682 AGCAGCGTGAACAAGAATGAAC 60.032 45.455 0.00 0.00 0.00 3.18
2479 5686 2.286950 GCAGCGTGAACAAGAATGAACA 60.287 45.455 0.00 0.00 0.00 3.18
2483 5690 5.288232 CAGCGTGAACAAGAATGAACAAAAA 59.712 36.000 0.00 0.00 0.00 1.94
2505 5713 7.769272 AAAATAATTGAATAACATGGCCGTG 57.231 32.000 23.83 23.83 0.00 4.94
2522 5730 2.031245 CCGTGAAAGTGCAGCACATAAA 60.031 45.455 27.35 7.56 36.74 1.40
2523 5731 2.973224 CGTGAAAGTGCAGCACATAAAC 59.027 45.455 27.35 17.45 36.74 2.01
2529 5737 3.916761 AGTGCAGCACATAAACAAATGG 58.083 40.909 27.35 0.00 36.74 3.16
2531 5739 3.674753 GTGCAGCACATAAACAAATGGAC 59.325 43.478 21.22 0.00 34.08 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.560025 GGGGATGAAGCTCTCAGACAAAA 60.560 47.826 0.00 0.00 37.52 2.44
34 35 0.388659 CTCGGGGATGAAGCTCTCAG 59.611 60.000 0.00 0.00 37.52 3.35
95 96 4.320023 TCATTGGTATTACAAGTGCACGT 58.680 39.130 12.01 5.01 33.23 4.49
117 118 0.178961 GGGGGTTTCCAACAGCTTCT 60.179 55.000 0.00 0.00 37.22 2.85
172 2330 1.271934 CACGCCCATCATTGGACAAAA 59.728 47.619 0.00 0.00 46.92 2.44
180 2338 1.315257 GCTCCAACACGCCCATCATT 61.315 55.000 0.00 0.00 0.00 2.57
214 2372 0.034896 GTGACCGTGTTCATCCCTGT 59.965 55.000 0.00 0.00 0.00 4.00
235 2393 1.753073 CAATTGATGAGGACCCAAGGC 59.247 52.381 0.00 0.00 0.00 4.35
259 2417 2.793288 AGGGTTAATAACACCGGGTG 57.207 50.000 25.21 25.21 39.75 4.61
296 2454 5.243981 GTCTCTAAAACTGTAGGGTTTCCC 58.756 45.833 0.00 0.00 45.90 3.97
297 2455 5.221783 TGGTCTCTAAAACTGTAGGGTTTCC 60.222 44.000 0.00 0.00 38.30 3.13
298 2456 5.861727 TGGTCTCTAAAACTGTAGGGTTTC 58.138 41.667 0.00 0.00 38.30 2.78
299 2457 5.899631 TGGTCTCTAAAACTGTAGGGTTT 57.100 39.130 0.00 0.00 40.59 3.27
300 2458 6.238648 CAATGGTCTCTAAAACTGTAGGGTT 58.761 40.000 0.00 0.00 0.00 4.11
301 2459 5.803470 GCAATGGTCTCTAAAACTGTAGGGT 60.803 44.000 0.00 0.00 0.00 4.34
302 2460 4.636206 GCAATGGTCTCTAAAACTGTAGGG 59.364 45.833 0.00 0.00 0.00 3.53
303 2461 5.491982 AGCAATGGTCTCTAAAACTGTAGG 58.508 41.667 0.00 0.00 0.00 3.18
304 2462 6.428159 ACAAGCAATGGTCTCTAAAACTGTAG 59.572 38.462 0.00 0.00 0.00 2.74
305 2463 6.296026 ACAAGCAATGGTCTCTAAAACTGTA 58.704 36.000 0.00 0.00 0.00 2.74
329 2487 1.795768 CAAGTGCTAAAGCCTCACGA 58.204 50.000 0.00 0.00 41.18 4.35
391 2549 6.325387 ATGATGTCATCCACAATCGGTTTGT 61.325 40.000 10.36 0.00 39.73 2.83
504 2662 3.005554 CCTCATCATTTGAAGCACGACT 58.994 45.455 0.00 0.00 32.78 4.18
515 2673 4.178540 CAAAATTGCGAGCCTCATCATTT 58.821 39.130 0.00 0.00 0.00 2.32
519 2677 2.927553 ACAAAATTGCGAGCCTCATC 57.072 45.000 0.00 0.00 0.00 2.92
628 3205 6.183360 GGCCTAGGAGTAGTACAGTTTACTTC 60.183 46.154 14.75 0.00 30.58 3.01
680 3260 1.007849 CCCCCTTTGTTGTTTCGCG 60.008 57.895 0.00 0.00 0.00 5.87
681 3261 0.747852 TTCCCCCTTTGTTGTTTCGC 59.252 50.000 0.00 0.00 0.00 4.70
854 3743 2.619074 GGTCACATGGAGGGAAAGGAAG 60.619 54.545 0.00 0.00 0.00 3.46
855 3744 1.354368 GGTCACATGGAGGGAAAGGAA 59.646 52.381 0.00 0.00 0.00 3.36
856 3745 0.991920 GGTCACATGGAGGGAAAGGA 59.008 55.000 0.00 0.00 0.00 3.36
857 3746 0.034089 GGGTCACATGGAGGGAAAGG 60.034 60.000 0.00 0.00 0.00 3.11
919 3808 1.306482 TTGGAGCTGGAGGAGGAGG 60.306 63.158 0.00 0.00 0.00 4.30
920 3809 0.325110 TCTTGGAGCTGGAGGAGGAG 60.325 60.000 0.00 0.00 0.00 3.69
921 3810 0.117140 TTCTTGGAGCTGGAGGAGGA 59.883 55.000 0.00 0.00 0.00 3.71
922 3811 0.251634 GTTCTTGGAGCTGGAGGAGG 59.748 60.000 0.00 0.00 0.00 4.30
956 3857 2.546494 CGGGAATGCGGCTTGGATC 61.546 63.158 0.00 0.00 0.00 3.36
963 3864 2.660258 ATCTGGTACGGGAATGCGGC 62.660 60.000 0.00 0.00 33.92 6.53
966 3867 1.222115 GCGATCTGGTACGGGAATGC 61.222 60.000 0.00 0.00 33.92 3.56
985 3887 2.758089 GCTGATTGGTGGCGAGCTG 61.758 63.158 0.00 0.00 0.00 4.24
994 3896 1.210478 AGTAATCCGCAGCTGATTGGT 59.790 47.619 20.43 6.10 34.43 3.67
1000 3902 1.565305 GACTGAGTAATCCGCAGCTG 58.435 55.000 10.11 10.11 33.03 4.24
1001 3903 0.461961 GGACTGAGTAATCCGCAGCT 59.538 55.000 0.00 0.00 33.03 4.24
1002 3904 0.461961 AGGACTGAGTAATCCGCAGC 59.538 55.000 0.00 0.00 40.20 5.25
1018 3920 1.028905 CCACGGAAACAAAGCAAGGA 58.971 50.000 0.00 0.00 0.00 3.36
1026 3928 2.535788 CGCGAACCCACGGAAACAA 61.536 57.895 0.00 0.00 0.00 2.83
1409 4311 1.377463 CACTCCTCCGACTCCTCGT 60.377 63.158 0.00 0.00 38.32 4.18
1480 4382 1.458639 AAACAGCAGCAGCCTGAACC 61.459 55.000 5.73 0.00 41.77 3.62
1637 4544 1.261619 GAAGAATCATACAAGCGGCGG 59.738 52.381 9.78 0.00 0.00 6.13
1663 4570 4.950205 TCCCTTTCGAAGTGTACTCTTT 57.050 40.909 11.27 0.00 0.00 2.52
1693 4600 4.410228 AGACAATGGTGCACTATGACCTAT 59.590 41.667 17.16 0.00 32.98 2.57
1695 4602 2.573462 AGACAATGGTGCACTATGACCT 59.427 45.455 17.16 10.49 32.98 3.85
1703 4661 4.568152 AAGTTGTTAGACAATGGTGCAC 57.432 40.909 8.80 8.80 40.59 4.57
1708 4666 5.048713 GGGTCTGAAAGTTGTTAGACAATGG 60.049 44.000 13.28 0.00 40.59 3.16
1721 4679 5.304686 TGTATGACTTTGGGTCTGAAAGT 57.695 39.130 0.00 0.00 44.51 2.66
1725 4683 6.406370 CAAGTATGTATGACTTTGGGTCTGA 58.594 40.000 0.00 0.00 44.74 3.27
1736 4694 8.004087 TCACCTTACTACCAAGTATGTATGAC 57.996 38.462 0.00 0.00 38.02 3.06
1737 4695 8.057011 TCTCACCTTACTACCAAGTATGTATGA 58.943 37.037 0.00 0.00 38.02 2.15
1738 4696 8.234136 TCTCACCTTACTACCAAGTATGTATG 57.766 38.462 0.00 0.00 38.02 2.39
1739 4697 8.834004 TTCTCACCTTACTACCAAGTATGTAT 57.166 34.615 0.00 0.00 38.02 2.29
1740 4698 8.654485 TTTCTCACCTTACTACCAAGTATGTA 57.346 34.615 0.00 0.00 38.02 2.29
1741 4699 7.549147 TTTCTCACCTTACTACCAAGTATGT 57.451 36.000 0.00 0.00 38.02 2.29
1742 4700 8.478877 AGATTTCTCACCTTACTACCAAGTATG 58.521 37.037 0.00 0.00 38.02 2.39
1743 4701 8.478877 CAGATTTCTCACCTTACTACCAAGTAT 58.521 37.037 0.00 0.00 38.02 2.12
1750 4792 8.496751 GTTGTTTCAGATTTCTCACCTTACTAC 58.503 37.037 0.00 0.00 0.00 2.73
1754 4796 7.012327 CACTGTTGTTTCAGATTTCTCACCTTA 59.988 37.037 0.65 0.00 38.63 2.69
1761 4803 7.275920 AGAGTACACTGTTGTTTCAGATTTCT 58.724 34.615 0.00 0.00 38.63 2.52
1767 4809 6.042777 TGAAGAGAGTACACTGTTGTTTCAG 58.957 40.000 7.42 0.00 40.80 3.02
1768 4810 5.972935 TGAAGAGAGTACACTGTTGTTTCA 58.027 37.500 7.42 0.00 37.15 2.69
1770 4812 5.360591 CCTGAAGAGAGTACACTGTTGTTT 58.639 41.667 7.42 0.00 37.15 2.83
1783 4825 3.910568 ATTCTCCAAGCCTGAAGAGAG 57.089 47.619 0.00 0.00 36.76 3.20
1789 4831 5.483937 TCTTGTAGTTATTCTCCAAGCCTGA 59.516 40.000 0.00 0.00 39.12 3.86
1790 4832 5.734720 TCTTGTAGTTATTCTCCAAGCCTG 58.265 41.667 0.00 0.00 39.12 4.85
1791 4833 6.567602 ATCTTGTAGTTATTCTCCAAGCCT 57.432 37.500 0.00 0.00 39.12 4.58
1792 4834 7.631717 AAATCTTGTAGTTATTCTCCAAGCC 57.368 36.000 0.00 0.00 39.12 4.35
1793 4835 8.730680 TGAAAATCTTGTAGTTATTCTCCAAGC 58.269 33.333 0.00 0.00 39.12 4.01
1795 4837 9.010029 GGTGAAAATCTTGTAGTTATTCTCCAA 57.990 33.333 0.00 0.00 32.24 3.53
1804 4857 2.482721 CGCGGGTGAAAATCTTGTAGTT 59.517 45.455 0.00 0.00 0.00 2.24
1805 4858 2.073816 CGCGGGTGAAAATCTTGTAGT 58.926 47.619 0.00 0.00 0.00 2.73
1811 4864 2.045340 CCCCGCGGGTGAAAATCT 60.045 61.111 40.52 0.00 38.25 2.40
1815 4868 4.669809 AATGCCCCGCGGGTGAAA 62.670 61.111 40.52 23.75 46.51 2.69
1828 4881 4.913924 GGCATATTCTTGTGAATCGAATGC 59.086 41.667 12.72 12.72 43.93 3.56
1836 4922 5.015515 TCAACATGGGCATATTCTTGTGAA 58.984 37.500 0.00 0.00 36.54 3.18
1845 4958 4.796110 ACTAAGGTCAACATGGGCATAT 57.204 40.909 0.00 0.00 0.00 1.78
1918 5075 6.000219 ACTTCTGAATGTTGTGCTATCAGTT 59.000 36.000 0.00 0.00 38.83 3.16
1954 5111 4.692625 CGTTTCAGGAAGATGTCAGACAAT 59.307 41.667 7.50 0.00 0.00 2.71
1968 5125 3.389925 AAATACACCGTCGTTTCAGGA 57.610 42.857 0.00 0.00 0.00 3.86
1969 5126 3.744426 AGAAAATACACCGTCGTTTCAGG 59.256 43.478 6.54 0.00 31.94 3.86
1970 5127 4.432503 CGAGAAAATACACCGTCGTTTCAG 60.433 45.833 6.54 0.00 31.94 3.02
1980 5171 7.591006 TCACAGATTTACGAGAAAATACACC 57.409 36.000 0.00 0.00 0.00 4.16
1997 5188 2.306805 TGAAGCCAGGACATTCACAGAT 59.693 45.455 0.00 0.00 0.00 2.90
1998 5189 1.699083 TGAAGCCAGGACATTCACAGA 59.301 47.619 0.00 0.00 0.00 3.41
1999 5190 2.082231 CTGAAGCCAGGACATTCACAG 58.918 52.381 0.00 0.00 36.77 3.66
2000 5191 1.699083 TCTGAAGCCAGGACATTCACA 59.301 47.619 0.00 0.00 40.76 3.58
2062 5262 3.621715 CGTAGCACCTTTATTCCCTGTTC 59.378 47.826 0.00 0.00 0.00 3.18
2065 5265 3.261981 ACGTAGCACCTTTATTCCCTG 57.738 47.619 0.00 0.00 0.00 4.45
2067 5267 5.448225 GCTAAAACGTAGCACCTTTATTCCC 60.448 44.000 3.93 0.00 40.14 3.97
2068 5268 5.353400 AGCTAAAACGTAGCACCTTTATTCC 59.647 40.000 11.19 0.00 42.68 3.01
2069 5269 6.418585 AGCTAAAACGTAGCACCTTTATTC 57.581 37.500 11.19 0.00 42.68 1.75
2070 5270 5.063060 CGAGCTAAAACGTAGCACCTTTATT 59.937 40.000 11.19 0.00 42.68 1.40
2121 5321 2.487934 ACACATGATCTAATGAGCGCC 58.512 47.619 2.29 0.00 0.00 6.53
2156 5362 7.492352 AGCAGAACGTTTTACTTATTTGTCT 57.508 32.000 0.46 0.00 0.00 3.41
2195 5402 4.887655 GCCTTGCCACTACCATAACTATTT 59.112 41.667 0.00 0.00 0.00 1.40
2197 5404 3.716872 AGCCTTGCCACTACCATAACTAT 59.283 43.478 0.00 0.00 0.00 2.12
2198 5405 3.112263 AGCCTTGCCACTACCATAACTA 58.888 45.455 0.00 0.00 0.00 2.24
2199 5406 1.916181 AGCCTTGCCACTACCATAACT 59.084 47.619 0.00 0.00 0.00 2.24
2210 5417 1.377725 GCTGCTTAGAGCCTTGCCA 60.378 57.895 0.00 0.00 41.51 4.92
2212 5419 1.065251 GAATGCTGCTTAGAGCCTTGC 59.935 52.381 0.00 0.89 41.51 4.01
2274 5481 1.337071 TGCTAGCTTTACCGGAGATCG 59.663 52.381 17.23 0.00 38.88 3.69
2275 5482 2.362717 ACTGCTAGCTTTACCGGAGATC 59.637 50.000 17.23 0.00 0.00 2.75
2288 5495 1.876156 ACAGAACAAAGCACTGCTAGC 59.124 47.619 8.10 8.10 38.25 3.42
2290 5497 3.540617 TCAACAGAACAAAGCACTGCTA 58.459 40.909 3.33 0.00 38.25 3.49
2291 5498 2.368439 TCAACAGAACAAAGCACTGCT 58.632 42.857 0.00 0.00 42.56 4.24
2305 5512 3.379372 CCAGAGGCCAATGTAATCAACAG 59.621 47.826 5.01 0.00 42.70 3.16
2306 5513 3.355378 CCAGAGGCCAATGTAATCAACA 58.645 45.455 5.01 0.00 43.86 3.33
2380 5587 2.943978 AAGGTGGTCGGCTTCGAGG 61.944 63.158 0.00 0.00 44.17 4.63
2426 5633 4.311606 TGAAACGATGCTGCAGTTACTTA 58.688 39.130 16.64 0.00 0.00 2.24
2438 5645 2.848302 GCTAAACATGCTGAAACGATGC 59.152 45.455 0.00 0.00 0.00 3.91
2439 5646 4.082274 TGCTAAACATGCTGAAACGATG 57.918 40.909 0.00 0.00 0.00 3.84
2442 5649 2.245096 GCTGCTAAACATGCTGAAACG 58.755 47.619 0.00 0.00 0.00 3.60
2447 5654 0.798159 TCACGCTGCTAAACATGCTG 59.202 50.000 0.00 0.00 0.00 4.41
2483 5690 6.707440 TCACGGCCATGTTATTCAATTATT 57.293 33.333 2.24 0.00 0.00 1.40
2495 5702 1.518056 CTGCACTTTCACGGCCATGT 61.518 55.000 2.24 0.00 0.00 3.21
2498 5705 3.286751 GCTGCACTTTCACGGCCA 61.287 61.111 2.24 0.00 31.76 5.36
2503 5711 3.963665 TGTTTATGTGCTGCACTTTCAC 58.036 40.909 30.43 22.26 35.11 3.18
2505 5713 5.107375 CCATTTGTTTATGTGCTGCACTTTC 60.107 40.000 30.43 18.14 35.11 2.62


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

AutoCloner maintained by Alex Coulton.