Multiple sequence alignment - TraesCS2A01G550200

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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 TraesCS2A01G550200 chr2A 100.000 5135 0 0 1 5135 757638375 757633241 0.000000e+00 9483.0
1 TraesCS2A01G550200 chr2D 95.211 4072 144 17 180 4228 626810959 626806916 0.000000e+00 6392.0
2 TraesCS2A01G550200 chr2D 91.106 416 30 3 4286 4695 626804770 626804356 1.620000e-154 556.0
3 TraesCS2A01G550200 chr2D 90.476 273 24 1 4861 5133 626805999 626805729 4.890000e-95 359.0
4 TraesCS2A01G550200 chr2D 90.351 228 17 3 4257 4480 626806919 626806693 1.400000e-75 294.0
5 TraesCS2A01G550200 chr2D 90.526 190 6 7 1 190 626811290 626811113 1.850000e-59 241.0
6 TraesCS2A01G550200 chr2D 88.235 102 6 4 4687 4788 626806120 626806025 3.250000e-22 117.0
7 TraesCS2A01G550200 chr2B 95.139 3559 159 3 686 4238 768289431 768292981 0.000000e+00 5602.0
8 TraesCS2A01G550200 chr2B 83.005 965 110 29 1702 2632 769552126 769551182 0.000000e+00 824.0
9 TraesCS2A01G550200 chr2B 88.280 529 16 13 38 542 768288526 768289032 4.430000e-165 592.0
10 TraesCS2A01G550200 chr2B 89.451 455 37 5 4242 4689 768292959 768293409 9.650000e-157 564.0
11 TraesCS2A01G550200 chr2B 87.583 451 36 12 4687 5135 768128912 768128480 5.930000e-139 505.0
12 TraesCS2A01G550200 chr2B 87.390 341 36 3 4354 4689 768129493 768129155 8.070000e-103 385.0
13 TraesCS2A01G550200 chr2B 88.479 217 22 3 2682 2895 769551106 769550890 5.100000e-65 259.0
14 TraesCS2A01G550200 chr2B 81.073 317 38 6 1267 1583 769552445 769552151 3.090000e-57 233.0
15 TraesCS2A01G550200 chr2B 85.556 180 23 1 1372 1548 769557822 769557643 8.780000e-43 185.0
16 TraesCS2A01G550200 chr2B 82.051 78 10 2 1728 1801 769557930 769557853 4.290000e-06 63.9


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 TraesCS2A01G550200 chr2A 757633241 757638375 5134 True 9483.000000 9483 100.000000 1 5135 1 chr2A.!!$R1 5134
1 TraesCS2A01G550200 chr2D 626804356 626811290 6934 True 1326.500000 6392 90.984167 1 5133 6 chr2D.!!$R1 5132
2 TraesCS2A01G550200 chr2B 768288526 768293409 4883 False 2252.666667 5602 90.956667 38 4689 3 chr2B.!!$F1 4651
3 TraesCS2A01G550200 chr2B 768128480 768129493 1013 True 445.000000 505 87.486500 4354 5135 2 chr2B.!!$R1 781
4 TraesCS2A01G550200 chr2B 769550890 769552445 1555 True 438.666667 824 84.185667 1267 2895 3 chr2B.!!$R2 1628

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
848 1294 0.385974 GTGTTTGCCATCTGTGCGTC 60.386 55.0 0.0 0.0 0.00 5.19 F
2121 2588 0.320247 AGCTGAAGACGCTGAACCTG 60.320 55.0 0.0 0.0 36.15 4.00 F
3411 3943 0.251832 TCGAGAGGGAGTTTCAGGCT 60.252 55.0 0.0 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2628 3154 0.250901 CTTGGTTGTACTGCAGGCCT 60.251 55.0 19.93 0.00 0.0 5.19 R
3468 4000 0.882484 TGTCGTTGCCGATCTTGCAA 60.882 50.0 13.58 13.58 46.3 4.08 R
4745 5657 0.254462 TGCAGACAACAGAACCACCA 59.746 50.0 0.00 0.00 0.0 4.17 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 7.724305 TTTCAACAGTCCAACTCAACTATAC 57.276 36.000 0.00 0.00 0.00 1.47
53 54 5.466819 TCAACAGTCCAACTCAACTATACG 58.533 41.667 0.00 0.00 0.00 3.06
76 78 5.510323 CGACGGTTTTCATAAATGTTAAGCC 59.490 40.000 0.00 0.00 0.00 4.35
88 90 8.818057 CATAAATGTTAAGCCAGTACAGTACTC 58.182 37.037 10.54 0.84 36.76 2.59
89 91 6.607004 AATGTTAAGCCAGTACAGTACTCT 57.393 37.500 10.54 3.28 36.76 3.24
90 92 5.386958 TGTTAAGCCAGTACAGTACTCTG 57.613 43.478 10.54 6.36 46.18 3.35
92 94 5.715279 TGTTAAGCCAGTACAGTACTCTGAT 59.285 40.000 10.54 1.15 43.76 2.90
96 98 6.398234 AGCCAGTACAGTACTCTGATTATG 57.602 41.667 10.54 0.00 43.76 1.90
115 119 9.890629 TGATTATGAGCAATCTTACACTTTACT 57.109 29.630 0.00 0.00 36.16 2.24
128 132 9.706691 TCTTACACTTTACTCTAGTTTTCATGG 57.293 33.333 0.00 0.00 0.00 3.66
149 153 4.291047 CGTGCAATGGAGTGCTCT 57.709 55.556 0.32 0.00 45.17 4.09
186 190 5.757320 TCAAACAAGTTATGGGCAACATTTG 59.243 36.000 0.00 1.31 41.03 2.32
387 571 3.892588 TGGTTTCTGTCCGCCTTTTATTT 59.107 39.130 0.00 0.00 0.00 1.40
388 572 4.342665 TGGTTTCTGTCCGCCTTTTATTTT 59.657 37.500 0.00 0.00 0.00 1.82
389 573 5.535406 TGGTTTCTGTCCGCCTTTTATTTTA 59.465 36.000 0.00 0.00 0.00 1.52
390 574 6.209788 TGGTTTCTGTCCGCCTTTTATTTTAT 59.790 34.615 0.00 0.00 0.00 1.40
391 575 7.094631 GGTTTCTGTCCGCCTTTTATTTTATT 58.905 34.615 0.00 0.00 0.00 1.40
392 576 8.245491 GGTTTCTGTCCGCCTTTTATTTTATTA 58.755 33.333 0.00 0.00 0.00 0.98
393 577 9.797556 GTTTCTGTCCGCCTTTTATTTTATTAT 57.202 29.630 0.00 0.00 0.00 1.28
478 665 3.423154 GCGCACGGGAAAGTCCAG 61.423 66.667 0.30 0.00 38.64 3.86
591 778 2.529389 AGTGCCCGTCCCTTTCCT 60.529 61.111 0.00 0.00 0.00 3.36
773 1219 4.659172 CCCTTGCTTCCGCCACCA 62.659 66.667 0.00 0.00 34.43 4.17
794 1240 1.298713 CTCTGCTCGTCGGGATTCG 60.299 63.158 0.00 0.00 40.90 3.34
803 1249 1.000145 GTCGGGATTCGCTTGAGTTC 59.000 55.000 0.00 0.00 39.05 3.01
848 1294 0.385974 GTGTTTGCCATCTGTGCGTC 60.386 55.000 0.00 0.00 0.00 5.19
852 1298 0.955428 TTGCCATCTGTGCGTCCTTC 60.955 55.000 0.00 0.00 0.00 3.46
854 1300 1.450312 CCATCTGTGCGTCCTTCCC 60.450 63.158 0.00 0.00 0.00 3.97
1204 1651 4.767255 GGTCGTGCTGCTCCTGGG 62.767 72.222 0.00 0.00 0.00 4.45
1463 1910 3.202706 GTTCCCGGCGATTGAGGC 61.203 66.667 9.30 0.00 0.00 4.70
1587 2034 4.235762 AACACCACCGCGCTCTGT 62.236 61.111 5.56 0.00 0.00 3.41
1745 2192 2.742372 CCTGTACACGGTGCCTGC 60.742 66.667 8.30 0.00 0.00 4.85
1746 2193 3.112075 CTGTACACGGTGCCTGCG 61.112 66.667 8.30 0.00 0.00 5.18
1747 2194 3.858868 CTGTACACGGTGCCTGCGT 62.859 63.158 8.30 0.00 0.00 5.24
1879 2326 0.967380 CCCTGATGTGTTTGGGAGGC 60.967 60.000 0.00 0.00 42.11 4.70
1886 2333 0.322008 GTGTTTGGGAGGCTGAGGAG 60.322 60.000 0.00 0.00 0.00 3.69
1894 2341 2.441164 GGCTGAGGAGGCTCGAGA 60.441 66.667 18.75 0.00 41.64 4.04
1955 2408 1.524355 CAGTTCACTGTCAAGCTGTCG 59.476 52.381 0.00 0.00 39.09 4.35
1960 2413 0.681733 ACTGTCAAGCTGTCGGATGT 59.318 50.000 0.00 0.00 0.00 3.06
2058 2516 1.880027 ACTTTCGATGCTGGGTCAAAC 59.120 47.619 0.00 0.00 0.00 2.93
2121 2588 0.320247 AGCTGAAGACGCTGAACCTG 60.320 55.000 0.00 0.00 36.15 4.00
2143 2610 1.067354 CAAGGAACAAGCTTGATGGGC 60.067 52.381 32.50 15.04 0.00 5.36
2178 2645 7.220030 AGAGCTTCAAGAATTTGAGTTCACTA 58.780 34.615 0.00 0.00 43.76 2.74
2227 2694 0.740868 CACGAACCTGTCATCGGCAT 60.741 55.000 0.00 0.00 43.11 4.40
2379 2857 3.039202 GCTCACCGGCACAATTCCG 62.039 63.158 0.00 0.00 46.05 4.30
2395 2873 4.711949 CGCCTTGGCTGCAGACCT 62.712 66.667 19.23 0.00 0.00 3.85
2397 2875 2.633509 GCCTTGGCTGCAGACCTTG 61.634 63.158 19.23 13.40 0.00 3.61
2938 3467 2.989253 CAACCGGGGGCCAGTTTC 60.989 66.667 6.32 0.00 0.00 2.78
3045 3574 1.871039 GAAGCAGCACACCGTAAGAAA 59.129 47.619 0.00 0.00 43.02 2.52
3411 3943 0.251832 TCGAGAGGGAGTTTCAGGCT 60.252 55.000 0.00 0.00 0.00 4.58
3468 4000 0.251297 TTGTGTTGCTGCAGGGCTAT 60.251 50.000 17.12 0.00 0.00 2.97
3711 4243 1.831580 ACTTTGAAGCTCATCTGGCC 58.168 50.000 0.00 0.00 0.00 5.36
3744 4276 1.519455 GAGGCTTGTCTGCGCGTAT 60.519 57.895 8.43 0.00 0.00 3.06
3762 4294 2.359967 TGACACCCACGTCACCACA 61.360 57.895 0.00 0.00 40.94 4.17
3954 4486 3.779183 TGCTTCAGATGAGGAAAGAGGAT 59.221 43.478 0.00 0.00 0.00 3.24
3999 4531 2.443887 ATGTGCATGACAAGGCAAAC 57.556 45.000 6.72 0.00 46.14 2.93
4032 4564 1.219124 GAGGGTGCTCGAGATTGCA 59.781 57.895 18.75 4.47 36.79 4.08
4068 4600 4.299796 GCCCCCAAGTCAAGGCCA 62.300 66.667 5.01 0.00 39.60 5.36
4071 4603 1.152567 CCCCAAGTCAAGGCCAACA 60.153 57.895 5.01 0.00 0.00 3.33
4190 4731 1.467734 GAGCAGAGCATCAGTTTGGTG 59.532 52.381 0.00 0.00 37.82 4.17
4191 4732 0.524862 GCAGAGCATCAGTTTGGTGG 59.475 55.000 0.00 0.00 37.82 4.61
4192 4733 1.901591 CAGAGCATCAGTTTGGTGGT 58.098 50.000 0.00 0.00 42.59 4.16
4356 4900 6.126863 TGAGCTTCCTCTTTTCCATAAAGA 57.873 37.500 0.00 0.00 38.93 2.52
4418 4964 5.248640 ACCATCTGGATAATAATCAAGCGG 58.751 41.667 2.55 0.00 33.65 5.52
4420 4966 5.352569 CCATCTGGATAATAATCAAGCGGTC 59.647 44.000 0.00 0.00 33.65 4.79
4432 4978 1.936547 CAAGCGGTCTTATCTGAAGGC 59.063 52.381 0.00 0.00 0.00 4.35
4500 5152 9.892130 AGTTTTATGTTTGTGGGTGAATTTAAA 57.108 25.926 0.00 0.00 0.00 1.52
4535 5187 3.009363 TGACATCAAGAGCCAAAGGATGA 59.991 43.478 6.91 0.00 38.87 2.92
4556 5208 5.255687 TGATATGTTGTCTGCATGACCTTT 58.744 37.500 11.99 1.05 44.75 3.11
4570 5227 1.751351 GACCTTTGGCCTGCTATTTCC 59.249 52.381 3.32 0.00 0.00 3.13
4598 5256 2.906389 TCCCTGGGCATATCTGTGTATC 59.094 50.000 8.22 0.00 0.00 2.24
4647 5305 2.769663 TGTGACTTGACTAGTGGTTGGT 59.230 45.455 0.00 0.00 37.17 3.67
4652 5310 3.965347 ACTTGACTAGTGGTTGGTACTGT 59.035 43.478 0.00 0.00 35.19 3.55
4732 5644 7.468631 GCACTCACTAAACTTGAAGGATCAAAA 60.469 37.037 0.00 0.00 44.64 2.44
4734 5646 8.406297 ACTCACTAAACTTGAAGGATCAAAAAC 58.594 33.333 0.00 0.00 44.64 2.43
4735 5647 8.519799 TCACTAAACTTGAAGGATCAAAAACT 57.480 30.769 0.00 0.00 44.64 2.66
4736 5648 8.966868 TCACTAAACTTGAAGGATCAAAAACTT 58.033 29.630 0.00 0.00 44.64 2.66
4737 5649 9.237846 CACTAAACTTGAAGGATCAAAAACTTC 57.762 33.333 0.00 0.00 44.64 3.01
4739 5651 6.790232 AACTTGAAGGATCAAAAACTTCCA 57.210 33.333 0.00 0.00 44.64 3.53
4740 5652 6.983906 ACTTGAAGGATCAAAAACTTCCAT 57.016 33.333 0.00 0.00 44.64 3.41
4741 5653 6.986250 ACTTGAAGGATCAAAAACTTCCATC 58.014 36.000 0.00 0.00 44.64 3.51
4744 5656 5.711976 TGAAGGATCAAAAACTTCCATCCTC 59.288 40.000 0.00 0.00 42.18 3.71
4745 5657 5.527026 AGGATCAAAAACTTCCATCCTCT 57.473 39.130 0.00 0.00 39.38 3.69
4772 5684 0.583438 CTGTTGTCTGCACGACCTTG 59.417 55.000 11.99 0.00 42.13 3.61
4773 5685 0.107897 TGTTGTCTGCACGACCTTGT 60.108 50.000 11.99 0.00 42.13 3.16
4796 5730 2.123982 GCCTGCTGCCCTGCTATT 60.124 61.111 0.00 0.00 0.00 1.73
4797 5731 1.755783 GCCTGCTGCCCTGCTATTT 60.756 57.895 0.00 0.00 0.00 1.40
4798 5732 1.325476 GCCTGCTGCCCTGCTATTTT 61.325 55.000 0.00 0.00 0.00 1.82
4799 5733 1.188863 CCTGCTGCCCTGCTATTTTT 58.811 50.000 0.00 0.00 0.00 1.94
4855 5789 4.985538 ATCTGACTACTAGTTGGAACCG 57.014 45.455 0.00 0.00 0.00 4.44
4905 5839 3.303132 GGCAGATCAGGTATTAAAACGCG 60.303 47.826 3.53 3.53 0.00 6.01
5022 5956 0.466922 ATCAAGCATAGGCCTGGTGC 60.467 55.000 28.11 28.11 42.56 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 5.510323 GGCTTAACATTTATGAAAACCGTCG 59.490 40.000 0.00 0.00 0.00 5.12
53 54 6.383415 TGGCTTAACATTTATGAAAACCGTC 58.617 36.000 0.00 0.00 0.00 4.79
76 78 7.032377 TGCTCATAATCAGAGTACTGTACTG 57.968 40.000 24.15 12.28 43.81 2.74
89 91 9.890629 AGTAAAGTGTAAGATTGCTCATAATCA 57.109 29.630 0.00 0.00 39.08 2.57
96 98 8.989653 AACTAGAGTAAAGTGTAAGATTGCTC 57.010 34.615 0.00 0.00 36.44 4.26
114 118 3.557595 GCACGGATCCATGAAAACTAGAG 59.442 47.826 13.07 0.00 0.00 2.43
115 119 3.055458 TGCACGGATCCATGAAAACTAGA 60.055 43.478 13.07 0.00 0.00 2.43
116 120 3.270027 TGCACGGATCCATGAAAACTAG 58.730 45.455 13.07 0.00 0.00 2.57
117 121 3.342377 TGCACGGATCCATGAAAACTA 57.658 42.857 13.07 0.00 0.00 2.24
128 132 0.745845 AGCACTCCATTGCACGGATC 60.746 55.000 4.53 0.00 45.62 3.36
144 148 4.415881 TTGACTAGTGTGGAAAAGAGCA 57.584 40.909 0.00 0.00 0.00 4.26
149 153 6.827586 AACTTGTTTGACTAGTGTGGAAAA 57.172 33.333 0.00 0.00 34.57 2.29
186 190 0.037975 CATGCAGTTTTGGTGGCCTC 60.038 55.000 3.32 0.00 0.00 4.70
217 383 2.863153 GTGCATGGTCAGTGCGTC 59.137 61.111 0.00 0.00 45.37 5.19
389 573 9.878599 GCAGCGGCGATTAATAATAATAATAAT 57.121 29.630 12.98 0.00 31.83 1.28
390 574 8.884726 TGCAGCGGCGATTAATAATAATAATAA 58.115 29.630 12.98 0.00 45.35 1.40
391 575 8.426881 TGCAGCGGCGATTAATAATAATAATA 57.573 30.769 12.98 0.00 45.35 0.98
392 576 7.315247 TGCAGCGGCGATTAATAATAATAAT 57.685 32.000 12.98 0.00 45.35 1.28
393 577 6.729391 TGCAGCGGCGATTAATAATAATAA 57.271 33.333 12.98 0.00 45.35 1.40
394 578 6.714492 CATGCAGCGGCGATTAATAATAATA 58.286 36.000 12.98 0.00 45.35 0.98
435 619 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
436 620 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
475 662 4.087892 CTGTCTCCCCCACGCTGG 62.088 72.222 0.00 0.00 37.25 4.85
591 778 4.779733 GTCAGAGGGGCGGAGGGA 62.780 72.222 0.00 0.00 0.00 4.20
773 1219 1.608717 AATCCCGACGAGCAGAGCTT 61.609 55.000 0.00 0.00 39.88 3.74
817 1263 0.312102 GCAAACACTCCTCAGCAACC 59.688 55.000 0.00 0.00 0.00 3.77
852 1298 2.203070 CGGAGGAATCCAAGCGGG 60.203 66.667 0.61 0.00 38.37 6.13
1463 1910 1.137513 GTTGAAGGAGACGTTCACCG 58.862 55.000 6.42 0.00 44.03 4.94
1745 2192 0.390340 TAAGCTCAGCCTCTGCAACG 60.390 55.000 0.00 0.00 41.13 4.10
1746 2193 1.082690 GTAAGCTCAGCCTCTGCAAC 58.917 55.000 0.00 0.00 41.13 4.17
1747 2194 0.686789 TGTAAGCTCAGCCTCTGCAA 59.313 50.000 0.00 0.00 41.13 4.08
1791 2238 1.342174 GACAGGTTACCGAGGTTGTCA 59.658 52.381 15.91 0.00 34.28 3.58
1879 2326 0.682855 AAGGTCTCGAGCCTCCTCAG 60.683 60.000 23.06 0.00 38.00 3.35
1886 2333 2.347731 CCAAGTTTAAGGTCTCGAGCC 58.652 52.381 7.81 12.55 0.00 4.70
1890 2337 2.225727 GGTTGCCAAGTTTAAGGTCTCG 59.774 50.000 0.00 0.00 0.00 4.04
1936 2389 1.539065 CCGACAGCTTGACAGTGAACT 60.539 52.381 0.00 0.00 0.00 3.01
2121 2588 1.067354 CCATCAAGCTTGTTCCTTGCC 60.067 52.381 25.19 0.00 39.54 4.52
2143 2610 2.690497 TCTTGAAGCTCTCCGGTATCTG 59.310 50.000 0.00 0.00 0.00 2.90
2379 2857 2.282745 AAGGTCTGCAGCCAAGGC 60.283 61.111 23.46 2.02 42.33 4.35
2395 2873 1.123861 AGCACACTGAGGCTCTCCAA 61.124 55.000 16.72 0.00 34.76 3.53
2397 2875 3.386592 AGCACACTGAGGCTCTCC 58.613 61.111 16.72 0.00 34.76 3.71
2437 2915 1.144913 CCATCGGGGGATGTTACCATT 59.855 52.381 3.66 0.00 0.00 3.16
2535 3017 2.092968 TGAAATCAGACCCTTCATCCGG 60.093 50.000 0.00 0.00 0.00 5.14
2580 3064 3.578456 GGGACGTACTCGGTCGAA 58.422 61.111 0.00 0.00 41.85 3.71
2628 3154 0.250901 CTTGGTTGTACTGCAGGCCT 60.251 55.000 19.93 0.00 0.00 5.19
2709 3235 2.957402 TCACAAGATGACCAAAGCCT 57.043 45.000 0.00 0.00 29.99 4.58
2938 3467 1.267732 GCCTTCATTCGCGAATGTCAG 60.268 52.381 43.67 38.03 46.15 3.51
3019 3548 1.518056 CGGTGTGCTGCTTCCACAAT 61.518 55.000 15.65 0.00 44.01 2.71
3087 3616 3.396276 TCCACAAGACAAAGATAACCCCA 59.604 43.478 0.00 0.00 0.00 4.96
3411 3943 2.104792 CCTTGAAAGTGTCTCCACCTCA 59.895 50.000 0.00 0.00 42.88 3.86
3468 4000 0.882484 TGTCGTTGCCGATCTTGCAA 60.882 50.000 13.58 13.58 46.30 4.08
3597 4129 1.153756 CAACCCCCTTGCTGAACCT 59.846 57.895 0.00 0.00 0.00 3.50
3711 4243 1.878522 CCTCGCCAGTCCGAAATCG 60.879 63.158 0.00 0.00 36.72 3.34
3744 4276 2.304901 CTGTGGTGACGTGGGTGTCA 62.305 60.000 0.00 0.00 46.15 3.58
3762 4294 1.553690 CCAGGGTCCCAACGACATCT 61.554 60.000 11.55 0.00 43.95 2.90
3954 4486 1.203212 TGGAAAACCTCGGTCTCCCTA 60.203 52.381 12.28 0.00 0.00 3.53
3999 4531 2.884685 CTCAGCAGCTCGCCTTCG 60.885 66.667 0.00 0.00 44.04 3.79
4068 4600 0.886043 TGACAAGCTGCTGCGATGTT 60.886 50.000 23.37 12.42 45.42 2.71
4071 4603 2.037136 GGTGACAAGCTGCTGCGAT 61.037 57.895 1.35 0.37 45.42 4.58
4190 4731 1.303091 AACCATTTCACGGCGCTACC 61.303 55.000 6.90 0.00 0.00 3.18
4191 4732 1.361793 TAACCATTTCACGGCGCTAC 58.638 50.000 6.90 0.00 0.00 3.58
4192 4733 2.319136 ATAACCATTTCACGGCGCTA 57.681 45.000 6.90 0.00 0.00 4.26
4260 4801 9.941664 GTATTTCTCGCTATGTAAACACTACTA 57.058 33.333 0.00 0.00 0.00 1.82
4261 4802 8.684520 AGTATTTCTCGCTATGTAAACACTACT 58.315 33.333 0.00 0.00 0.00 2.57
4262 4803 8.744011 CAGTATTTCTCGCTATGTAAACACTAC 58.256 37.037 0.00 0.00 0.00 2.73
4263 4804 8.680001 TCAGTATTTCTCGCTATGTAAACACTA 58.320 33.333 0.00 0.00 0.00 2.74
4264 4805 7.544622 TCAGTATTTCTCGCTATGTAAACACT 58.455 34.615 0.00 0.00 0.00 3.55
4265 4806 7.701078 TCTCAGTATTTCTCGCTATGTAAACAC 59.299 37.037 0.00 0.00 0.00 3.32
4266 4807 7.768240 TCTCAGTATTTCTCGCTATGTAAACA 58.232 34.615 0.00 0.00 0.00 2.83
4356 4900 6.653526 TTTTTGTGACATTCCTGTGATCAT 57.346 33.333 0.00 0.00 35.14 2.45
4418 4964 6.150140 ACAAAACAGATGCCTTCAGATAAGAC 59.850 38.462 0.00 0.00 0.00 3.01
4420 4966 6.506500 ACAAAACAGATGCCTTCAGATAAG 57.493 37.500 0.00 0.00 0.00 1.73
4474 5126 9.892130 TTTAAATTCACCCACAAACATAAAACT 57.108 25.926 0.00 0.00 0.00 2.66
4499 5151 8.940952 GCTCTTGATGTCAAACTCTAAAGTATT 58.059 33.333 0.00 0.00 33.48 1.89
4500 5152 7.550906 GGCTCTTGATGTCAAACTCTAAAGTAT 59.449 37.037 0.00 0.00 33.48 2.12
4501 5153 6.874134 GGCTCTTGATGTCAAACTCTAAAGTA 59.126 38.462 0.00 0.00 33.48 2.24
4506 5158 4.890158 TGGCTCTTGATGTCAAACTCTA 57.110 40.909 0.00 0.00 35.15 2.43
4518 5170 5.378230 ACATATCATCCTTTGGCTCTTGA 57.622 39.130 0.00 0.00 0.00 3.02
4556 5208 0.704076 AACTGGGAAATAGCAGGCCA 59.296 50.000 5.01 0.00 0.00 5.36
4639 5297 3.947910 TGTAGCTACAGTACCAACCAC 57.052 47.619 22.67 0.00 0.00 4.16
4647 5305 9.938280 ATTTAGAACAACATTGTAGCTACAGTA 57.062 29.630 24.79 13.28 41.31 2.74
4652 5310 9.502091 AACTCATTTAGAACAACATTGTAGCTA 57.498 29.630 0.00 0.00 41.31 3.32
4685 5343 3.057033 GCCTTGCAGAGTGAAATGTCATT 60.057 43.478 0.00 0.00 35.80 2.57
4689 5347 1.610522 GTGCCTTGCAGAGTGAAATGT 59.389 47.619 0.00 0.00 40.08 2.71
4690 5348 1.884579 AGTGCCTTGCAGAGTGAAATG 59.115 47.619 0.00 0.00 40.08 2.32
4739 5651 2.039084 GACAACAGAACCACCAGAGGAT 59.961 50.000 0.00 0.00 0.00 3.24
4740 5652 1.416401 GACAACAGAACCACCAGAGGA 59.584 52.381 0.00 0.00 0.00 3.71
4741 5653 1.417890 AGACAACAGAACCACCAGAGG 59.582 52.381 0.00 0.00 0.00 3.69
4744 5656 0.947244 GCAGACAACAGAACCACCAG 59.053 55.000 0.00 0.00 0.00 4.00
4745 5657 0.254462 TGCAGACAACAGAACCACCA 59.746 50.000 0.00 0.00 0.00 4.17
4809 5743 6.513806 ACAGCACACATATATGCAGAAAAA 57.486 33.333 12.79 0.00 44.59 1.94
4810 5744 6.513806 AACAGCACACATATATGCAGAAAA 57.486 33.333 12.79 0.00 44.59 2.29
4811 5745 7.716560 AGATAACAGCACACATATATGCAGAAA 59.283 33.333 12.79 0.00 44.59 2.52
4812 5746 7.172019 CAGATAACAGCACACATATATGCAGAA 59.828 37.037 12.79 0.00 44.59 3.02
4813 5747 6.647895 CAGATAACAGCACACATATATGCAGA 59.352 38.462 12.79 0.00 44.59 4.26
4814 5748 6.647895 TCAGATAACAGCACACATATATGCAG 59.352 38.462 12.79 8.26 44.59 4.41
4815 5749 6.424812 GTCAGATAACAGCACACATATATGCA 59.575 38.462 12.79 0.00 44.59 3.96
4816 5750 6.648310 AGTCAGATAACAGCACACATATATGC 59.352 38.462 12.79 0.00 42.39 3.14
4822 5756 5.667539 AGTAGTCAGATAACAGCACACAT 57.332 39.130 0.00 0.00 0.00 3.21
4826 5760 6.037098 CCAACTAGTAGTCAGATAACAGCAC 58.963 44.000 2.58 0.00 0.00 4.40
4855 5789 9.606631 ATTTATCTGGAACAACTCTGTATCTTC 57.393 33.333 0.00 0.00 38.70 2.87
4905 5839 1.503542 CATTTGAGCAGGCACGTCC 59.496 57.895 0.00 0.00 0.00 4.79
5030 5964 4.618965 GGTGTTATACCGAATCAGAGACC 58.381 47.826 0.00 0.00 40.26 3.85


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

AutoCloner maintained by Alex Coulton.