Multiple sequence alignment - TraesCS7D01G290000

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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 TraesCS7D01G290000 chr7D 100.000 5810 0 0 1 5810 337560566 337554757 0.000000e+00 10730.0
1 TraesCS7D01G290000 chr7D 81.900 442 66 11 5350 5780 286667700 286667262 1.540000e-95 361.0
2 TraesCS7D01G290000 chr7D 100.000 30 0 0 2796 2825 337557653 337557624 8.130000e-04 56.5
3 TraesCS7D01G290000 chr7D 100.000 30 0 0 2914 2943 337557771 337557742 8.130000e-04 56.5
4 TraesCS7D01G290000 chr7B 95.743 4698 130 33 680 5349 346678602 346673947 0.000000e+00 7504.0
5 TraesCS7D01G290000 chr7B 92.365 668 34 6 1 666 346679238 346678586 0.000000e+00 935.0
6 TraesCS7D01G290000 chr7B 82.316 475 63 15 5350 5810 259788679 259788212 5.460000e-105 392.0
7 TraesCS7D01G290000 chr7A 96.407 4481 100 21 795 5237 360083101 360078644 0.000000e+00 7326.0
8 TraesCS7D01G290000 chr7A 93.804 581 32 3 5231 5810 360078595 360078018 0.000000e+00 870.0
9 TraesCS7D01G290000 chr7A 92.373 472 35 1 185 656 360109863 360109393 0.000000e+00 671.0
10 TraesCS7D01G290000 chr7A 90.476 84 6 2 693 776 360109390 360109309 6.160000e-20 110.0
11 TraesCS7D01G290000 chr7A 94.118 68 4 0 1 68 360180898 360180831 2.860000e-18 104.0
12 TraesCS7D01G290000 chr7A 100.000 30 0 0 2914 2943 360081083 360081054 8.130000e-04 56.5
13 TraesCS7D01G290000 chr5D 93.952 463 24 4 5349 5810 225528812 225529271 0.000000e+00 697.0
14 TraesCS7D01G290000 chr5D 92.918 466 28 4 5347 5810 225492988 225493450 0.000000e+00 673.0
15 TraesCS7D01G290000 chr4D 89.789 284 22 7 5530 5810 180345990 180345711 1.990000e-94 357.0
16 TraesCS7D01G290000 chr3B 81.116 466 59 16 5349 5792 323672585 323672127 4.310000e-91 346.0
17 TraesCS7D01G290000 chr3B 82.716 405 51 14 5349 5742 323682642 323682246 5.570000e-90 342.0
18 TraesCS7D01G290000 chr2A 80.376 479 68 21 5349 5810 296032870 296032401 2.010000e-89 340.0
19 TraesCS7D01G290000 chr2A 92.381 105 5 1 1574 1678 6501768 6501869 4.690000e-31 147.0
20 TraesCS7D01G290000 chr4A 80.000 450 67 18 5350 5785 277382136 277382576 1.570000e-80 311.0
21 TraesCS7D01G290000 chr1A 95.238 105 5 0 1574 1678 352174093 352174197 3.600000e-37 167.0
22 TraesCS7D01G290000 chr1A 92.593 108 8 0 1570 1677 188150957 188150850 7.800000e-34 156.0
23 TraesCS7D01G290000 chr1A 89.908 109 10 1 1571 1678 188149103 188148995 7.850000e-29 139.0
24 TraesCS7D01G290000 chr1D 90.826 109 10 0 1570 1678 128530426 128530318 4.690000e-31 147.0
25 TraesCS7D01G290000 chr4B 90.000 110 11 0 1569 1678 24556001 24555892 6.070000e-30 143.0
26 TraesCS7D01G290000 chr1B 90.654 107 10 0 1570 1676 229274841 229274735 6.070000e-30 143.0


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 TraesCS7D01G290000 chr7D 337554757 337560566 5809 True 3614.333333 10730 100.0000 1 5810 3 chr7D.!!$R2 5809
1 TraesCS7D01G290000 chr7B 346673947 346679238 5291 True 4219.500000 7504 94.0540 1 5349 2 chr7B.!!$R2 5348
2 TraesCS7D01G290000 chr7A 360078018 360083101 5083 True 2750.833333 7326 96.7370 795 5810 3 chr7A.!!$R2 5015
3 TraesCS7D01G290000 chr7A 360109309 360109863 554 True 390.500000 671 91.4245 185 776 2 chr7A.!!$R3 591

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
729 732 0.107017 TCAAATCAGCCCTAGCAGCC 60.107 55.000 0.00 0.0 43.56 4.85 F
952 959 1.281867 CCTAGGAGGCAAACACCATGA 59.718 52.381 1.05 0.0 0.00 3.07 F
1681 1688 1.801242 TTTCGGATGGAGGGAGCATA 58.199 50.000 0.00 0.0 0.00 3.14 F
2707 2733 2.422276 ATCTTCAGCGTTTGTTTGCC 57.578 45.000 0.00 0.0 0.00 4.52 F
3248 3292 0.542702 CCCCCAAAGCCAGTGTCATT 60.543 55.000 0.00 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 1977 0.257039 AATCCCAAGCCTGCTAGGTG 59.743 55.000 7.72 0.00 37.80 4.00 R
2511 2537 2.879756 GCCCCACGCCAATATCATACAT 60.880 50.000 0.00 0.00 0.00 2.29 R
3215 3259 0.251430 TGGGGGAACAAAATCCGTCC 60.251 55.000 0.00 0.00 40.62 4.79 R
3576 3623 2.355132 GCAGATGCAAACTCATCCTGAG 59.645 50.000 0.00 2.65 44.56 3.35 R
5065 5115 1.065928 CCCGCTCTACATCACCGTC 59.934 63.158 0.00 0.00 0.00 4.79 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 7.807977 AGTATCATCATCAAACCCAACATAC 57.192 36.000 0.00 0.00 0.00 2.39
30 31 4.928263 TCATCATCAAACCCAACATACCA 58.072 39.130 0.00 0.00 0.00 3.25
40 41 4.398319 ACCCAACATACCAACAGAAAGAG 58.602 43.478 0.00 0.00 0.00 2.85
41 42 4.104102 ACCCAACATACCAACAGAAAGAGA 59.896 41.667 0.00 0.00 0.00 3.10
42 43 5.222130 ACCCAACATACCAACAGAAAGAGAT 60.222 40.000 0.00 0.00 0.00 2.75
83 85 2.887568 GCCTCGTCGCTGGTGATG 60.888 66.667 6.10 0.00 0.00 3.07
98 100 1.211457 GTGATGGTGGATGAGCTCCTT 59.789 52.381 12.15 0.00 45.21 3.36
154 156 3.554544 CGGAGATGAGGGATGATTGACAG 60.555 52.174 0.00 0.00 0.00 3.51
171 173 1.269831 ACAGAGAGGACGCACAGAAAC 60.270 52.381 0.00 0.00 0.00 2.78
174 176 2.027625 GAGGACGCACAGAAACCGG 61.028 63.158 0.00 0.00 0.00 5.28
177 179 1.278637 GACGCACAGAAACCGGTTG 59.721 57.895 23.08 12.40 0.00 3.77
178 180 1.153329 ACGCACAGAAACCGGTTGA 60.153 52.632 23.08 0.00 0.00 3.18
189 191 1.204786 ACCGGTTGATGGTGGATGGA 61.205 55.000 0.00 0.00 38.60 3.41
355 357 4.310740 AGTGGGAATGAGGAATGGATAGT 58.689 43.478 0.00 0.00 0.00 2.12
372 374 5.202004 GGATAGTACAGGGAAGAAGAGTCA 58.798 45.833 0.00 0.00 0.00 3.41
401 403 3.461773 GGAGTGGCTAGAGCGGCA 61.462 66.667 1.45 0.00 43.26 5.69
409 411 1.586422 GCTAGAGCGGCATGATTTGA 58.414 50.000 1.45 0.00 0.00 2.69
475 477 2.394708 CGACAGACACGTCATCACTTT 58.605 47.619 0.00 0.00 35.54 2.66
476 478 2.153817 CGACAGACACGTCATCACTTTG 59.846 50.000 0.00 0.00 35.54 2.77
477 479 1.867233 ACAGACACGTCATCACTTTGC 59.133 47.619 0.00 0.00 0.00 3.68
520 522 2.254350 CGACTCCGTCTTGTCGCA 59.746 61.111 2.69 0.00 46.94 5.10
665 668 8.814038 ATTTATGTTGAGTTAGAGATGCCTTT 57.186 30.769 0.00 0.00 0.00 3.11
666 669 8.635765 TTTATGTTGAGTTAGAGATGCCTTTT 57.364 30.769 0.00 0.00 0.00 2.27
667 670 8.635765 TTATGTTGAGTTAGAGATGCCTTTTT 57.364 30.769 0.00 0.00 0.00 1.94
688 691 4.974645 TTTTTGCAGGGAGAGTTAGAGA 57.025 40.909 0.00 0.00 0.00 3.10
689 692 5.505181 TTTTTGCAGGGAGAGTTAGAGAT 57.495 39.130 0.00 0.00 0.00 2.75
690 693 4.478206 TTTGCAGGGAGAGTTAGAGATG 57.522 45.455 0.00 0.00 0.00 2.90
691 694 1.759445 TGCAGGGAGAGTTAGAGATGC 59.241 52.381 0.00 0.00 0.00 3.91
710 713 5.543790 AGATGCCCTTAACCTTGTTGAAAAT 59.456 36.000 0.00 0.00 0.00 1.82
729 732 0.107017 TCAAATCAGCCCTAGCAGCC 60.107 55.000 0.00 0.00 43.56 4.85
745 749 2.229062 GCAGCCAAAAACTTACTCCCTC 59.771 50.000 0.00 0.00 0.00 4.30
748 752 2.557056 GCCAAAAACTTACTCCCTCCAC 59.443 50.000 0.00 0.00 0.00 4.02
750 754 3.473625 CAAAAACTTACTCCCTCCACGT 58.526 45.455 0.00 0.00 0.00 4.49
751 755 3.851458 AAAACTTACTCCCTCCACGTT 57.149 42.857 0.00 0.00 0.00 3.99
783 787 9.781834 TTAGACTTTTTGTTGACATTAACAGTG 57.218 29.630 0.00 0.00 41.18 3.66
784 788 7.826690 AGACTTTTTGTTGACATTAACAGTGT 58.173 30.769 0.00 0.00 41.18 3.55
785 789 7.968405 AGACTTTTTGTTGACATTAACAGTGTC 59.032 33.333 0.00 1.47 44.77 3.67
834 838 3.806521 AGTAGTACTGTACCGCATCTACG 59.193 47.826 14.05 0.00 34.32 3.51
842 846 3.566742 TGTACCGCATCTACGTGTCATAT 59.433 43.478 0.00 0.00 0.00 1.78
851 855 6.626844 GCATCTACGTGTCATATCATCCATCT 60.627 42.308 0.00 0.00 0.00 2.90
857 861 7.845037 ACGTGTCATATCATCCATCTAATCAT 58.155 34.615 0.00 0.00 0.00 2.45
929 935 2.945008 GGAATCGACTGGCAATTCATGA 59.055 45.455 10.77 0.00 32.27 3.07
952 959 1.281867 CCTAGGAGGCAAACACCATGA 59.718 52.381 1.05 0.00 0.00 3.07
1681 1688 1.801242 TTTCGGATGGAGGGAGCATA 58.199 50.000 0.00 0.00 0.00 3.14
1750 1757 9.634163 AAGACAAGTTTTACTTTTGTTAGGTTG 57.366 29.630 0.00 0.00 36.03 3.77
1771 1778 6.423302 GGTTGATGACAAAACATGTGCAATTA 59.577 34.615 0.00 0.00 44.12 1.40
2073 2081 6.822667 ATCATAGCTCACATCTCTACAGAG 57.177 41.667 0.00 0.00 43.36 3.35
2074 2082 5.689835 TCATAGCTCACATCTCTACAGAGT 58.310 41.667 6.16 0.00 42.60 3.24
2124 2134 9.683069 CTACAGAAAACTTGCACAAATCTTAAT 57.317 29.630 0.00 0.00 0.00 1.40
2191 2201 3.254166 CAGAAGTAGTTGCAATGTGGCTT 59.746 43.478 0.59 3.52 34.04 4.35
2259 2269 9.547753 TTTAGCTCCTTTGTCAGATATTATGTC 57.452 33.333 0.00 0.00 0.00 3.06
2511 2537 6.662755 ACTATTGATTCATAAGTGGGCAAGA 58.337 36.000 1.73 0.00 0.00 3.02
2520 2546 7.315066 TCATAAGTGGGCAAGATGTATGATA 57.685 36.000 0.00 0.00 0.00 2.15
2707 2733 2.422276 ATCTTCAGCGTTTGTTTGCC 57.578 45.000 0.00 0.00 0.00 4.52
2722 2748 7.746475 CGTTTGTTTGCCTTTAAATGTTCAAAA 59.254 29.630 0.00 0.00 0.00 2.44
2908 2935 7.103641 TGTTGGTTTTTGCTGTTTACCATTTA 58.896 30.769 0.00 0.00 38.57 1.40
2909 2936 7.278868 TGTTGGTTTTTGCTGTTTACCATTTAG 59.721 33.333 0.00 0.00 38.57 1.85
2911 2938 6.981559 TGGTTTTTGCTGTTTACCATTTAGAC 59.018 34.615 0.00 0.00 34.13 2.59
2914 2941 8.354426 GTTTTTGCTGTTTACCATTTAGACCTA 58.646 33.333 0.00 0.00 0.00 3.08
2916 2943 9.742144 TTTTGCTGTTTACCATTTAGACCTATA 57.258 29.630 0.00 0.00 0.00 1.31
2917 2944 8.726870 TTGCTGTTTACCATTTAGACCTATAC 57.273 34.615 0.00 0.00 0.00 1.47
2918 2945 8.086143 TGCTGTTTACCATTTAGACCTATACT 57.914 34.615 0.00 0.00 0.00 2.12
2919 2946 9.204337 TGCTGTTTACCATTTAGACCTATACTA 57.796 33.333 0.00 0.00 0.00 1.82
3056 3083 7.552687 TGCCTTGTTTAGTAGGTTGAATATGAG 59.447 37.037 0.00 0.00 33.91 2.90
3105 3132 6.122850 TCGAAATATGCAAAATCTGTCCTG 57.877 37.500 0.00 0.00 0.00 3.86
3108 3135 6.690098 CGAAATATGCAAAATCTGTCCTGAAG 59.310 38.462 0.00 0.00 0.00 3.02
3109 3136 7.472334 AAATATGCAAAATCTGTCCTGAAGT 57.528 32.000 0.00 0.00 0.00 3.01
3119 3161 9.471702 AAAATCTGTCCTGAAGTGATTCATTAT 57.528 29.630 0.00 0.00 0.00 1.28
3181 3225 8.178313 GGATGTTTCTGCTCAAGTATTAAAGAC 58.822 37.037 0.00 0.00 0.00 3.01
3248 3292 0.542702 CCCCCAAAGCCAGTGTCATT 60.543 55.000 0.00 0.00 0.00 2.57
3263 3307 3.246226 GTGTCATTGCTACTATTCTGCCG 59.754 47.826 0.00 0.00 0.00 5.69
3305 3349 9.368416 AGTAGAAATGCTAGATAAGTGATACCA 57.632 33.333 0.00 0.00 0.00 3.25
3348 3392 7.565680 AGTATCACTAGTTCCATTGGTTTAGG 58.434 38.462 1.86 0.00 0.00 2.69
3388 3432 5.104652 AGCCTTATACATAACGGTGGTTTCT 60.105 40.000 0.00 0.00 37.58 2.52
3389 3433 5.007332 GCCTTATACATAACGGTGGTTTCTG 59.993 44.000 0.00 0.00 37.58 3.02
3426 3470 3.861840 CGTTGACTTGGATACTGACCAT 58.138 45.455 0.00 0.00 37.26 3.55
3516 3563 7.594015 ACACAACTAAACGTGATACAGTAGAAG 59.406 37.037 0.00 0.00 36.91 2.85
3575 3622 4.710423 TCTGTTGATAGTGTGAGCTCTC 57.290 45.455 16.19 12.36 0.00 3.20
3576 3623 3.445450 TCTGTTGATAGTGTGAGCTCTCC 59.555 47.826 16.19 6.15 0.00 3.71
3577 3624 3.435275 TGTTGATAGTGTGAGCTCTCCT 58.565 45.455 16.19 12.59 0.00 3.69
3706 3756 4.219033 GACTTATGTTTGAGGTTTGCACG 58.781 43.478 0.00 0.00 0.00 5.34
4544 4594 0.790814 GACAAAGAAAGACGGCGGAG 59.209 55.000 13.24 0.00 0.00 4.63
4708 4758 7.773149 AGATACTTCTGGTTACTGTGTGTATC 58.227 38.462 0.00 0.00 36.02 2.24
4950 5000 6.699204 CGCTCACAGTATTTAGATGATCAAGT 59.301 38.462 0.00 0.00 0.00 3.16
5028 5078 1.843851 TGGTTCTTCCCTGTCAAGTGT 59.156 47.619 0.00 0.00 34.77 3.55
5065 5115 2.922387 CTGTCACTGATCTCTGAAAGCG 59.078 50.000 0.00 0.00 0.00 4.68
5181 5231 4.783227 TCTGGTAAAGATTGCTACTCCCTT 59.217 41.667 0.00 0.00 0.00 3.95
5258 5366 2.050350 CACCATCTGGGGCTTGCTG 61.050 63.158 0.54 0.00 42.91 4.41
5264 5372 4.208403 TGGGGCTTGCTGTGCAGT 62.208 61.111 0.00 0.00 40.61 4.40
5359 5467 5.189928 TGTGTTGAACTGTTGTAACATCCT 58.810 37.500 17.51 0.00 38.41 3.24
5425 5533 6.541641 TGATTTAAAATTGGCTTGTGTTGCTT 59.458 30.769 0.00 0.00 0.00 3.91
5444 5552 8.012241 TGTTGCTTGTTGTTTGTAAATTTTGAC 58.988 29.630 0.00 0.00 0.00 3.18
5472 5580 9.108284 AGGATTTGAAACTTTTGGTGTTAAATG 57.892 29.630 0.00 0.00 0.00 2.32
5514 5622 8.547967 GGAATAAAAGGACTTTCCCAATTTTC 57.452 34.615 0.00 0.00 37.19 2.29
5592 5700 5.045869 TGACTTCCTGAATATTCCTTTCGGT 60.046 40.000 12.90 5.16 0.00 4.69
5606 5714 8.857694 ATTCCTTTCGGTCTTATTTTGAACTA 57.142 30.769 0.00 0.00 0.00 2.24
5677 5785 9.471702 ACATGACTTCCTCAAAGAATGATATTT 57.528 29.630 0.00 0.00 37.44 1.40
5685 5793 8.906867 TCCTCAAAGAATGATATTTGGTGAATC 58.093 33.333 4.00 0.00 38.11 2.52
5736 5844 9.231297 TCAACATTTAAAACAAATCCAACCAAA 57.769 25.926 0.00 0.00 0.00 3.28
5737 5845 9.846248 CAACATTTAAAACAAATCCAACCAAAA 57.154 25.926 0.00 0.00 0.00 2.44
5769 5878 9.308318 GAGAGAAGGTAATATGACTCTTTCAAC 57.692 37.037 0.00 0.00 37.92 3.18
5783 5892 4.743493 TCTTTCAACACAAAAGAGTTGGC 58.257 39.130 0.00 0.00 43.91 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.875726 TCTCATCTCTTTCTGTTGGTATGTTG 59.124 38.462 0.00 0.00 0.00 3.33
28 29 4.252073 CACCTCTCATCTCTTTCTGTTGG 58.748 47.826 0.00 0.00 0.00 3.77
30 31 3.326006 TGCACCTCTCATCTCTTTCTGTT 59.674 43.478 0.00 0.00 0.00 3.16
154 156 1.009389 CGGTTTCTGTGCGTCCTCTC 61.009 60.000 0.00 0.00 0.00 3.20
171 173 0.748005 GTCCATCCACCATCAACCGG 60.748 60.000 0.00 0.00 0.00 5.28
355 357 5.479375 ACGTTATTGACTCTTCTTCCCTGTA 59.521 40.000 0.00 0.00 0.00 2.74
372 374 3.975168 AGCCACTCCAACTACGTTATT 57.025 42.857 0.00 0.00 0.00 1.40
401 403 2.032550 CGCGCCTCTCATTTCAAATCAT 59.967 45.455 0.00 0.00 0.00 2.45
409 411 0.390860 ATCTAGCGCGCCTCTCATTT 59.609 50.000 30.33 9.26 0.00 2.32
460 462 0.859232 ACGCAAAGTGATGACGTGTC 59.141 50.000 0.00 0.00 33.85 3.67
475 477 0.941936 TTCGCACGAATCTTGACGCA 60.942 50.000 0.49 0.00 0.00 5.24
476 478 0.246912 CTTCGCACGAATCTTGACGC 60.247 55.000 5.87 0.00 33.28 5.19
477 479 1.060713 ACTTCGCACGAATCTTGACG 58.939 50.000 5.87 0.00 33.28 4.35
667 670 4.974645 TCTCTAACTCTCCCTGCAAAAA 57.025 40.909 0.00 0.00 0.00 1.94
668 671 4.836825 CATCTCTAACTCTCCCTGCAAAA 58.163 43.478 0.00 0.00 0.00 2.44
669 672 3.369892 GCATCTCTAACTCTCCCTGCAAA 60.370 47.826 0.00 0.00 0.00 3.68
670 673 2.169352 GCATCTCTAACTCTCCCTGCAA 59.831 50.000 0.00 0.00 0.00 4.08
671 674 1.759445 GCATCTCTAACTCTCCCTGCA 59.241 52.381 0.00 0.00 0.00 4.41
672 675 1.069978 GGCATCTCTAACTCTCCCTGC 59.930 57.143 0.00 0.00 0.00 4.85
673 676 1.691434 GGGCATCTCTAACTCTCCCTG 59.309 57.143 0.00 0.00 0.00 4.45
674 677 1.578215 AGGGCATCTCTAACTCTCCCT 59.422 52.381 0.00 0.00 37.77 4.20
675 678 2.095604 AGGGCATCTCTAACTCTCCC 57.904 55.000 0.00 0.00 0.00 4.30
676 679 4.202274 GGTTAAGGGCATCTCTAACTCTCC 60.202 50.000 0.00 0.00 0.00 3.71
677 680 4.651962 AGGTTAAGGGCATCTCTAACTCTC 59.348 45.833 0.00 0.00 0.00 3.20
678 681 4.625963 AGGTTAAGGGCATCTCTAACTCT 58.374 43.478 0.00 0.00 0.00 3.24
679 682 5.119694 CAAGGTTAAGGGCATCTCTAACTC 58.880 45.833 0.00 0.00 0.00 3.01
680 683 4.536489 ACAAGGTTAAGGGCATCTCTAACT 59.464 41.667 0.00 0.00 0.00 2.24
681 684 4.844884 ACAAGGTTAAGGGCATCTCTAAC 58.155 43.478 0.00 0.00 0.00 2.34
682 685 5.013704 TCAACAAGGTTAAGGGCATCTCTAA 59.986 40.000 0.00 0.00 0.00 2.10
683 686 4.534500 TCAACAAGGTTAAGGGCATCTCTA 59.466 41.667 0.00 0.00 0.00 2.43
684 687 3.330701 TCAACAAGGTTAAGGGCATCTCT 59.669 43.478 0.00 0.00 0.00 3.10
685 688 3.686016 TCAACAAGGTTAAGGGCATCTC 58.314 45.455 0.00 0.00 0.00 2.75
686 689 3.806949 TCAACAAGGTTAAGGGCATCT 57.193 42.857 0.00 0.00 0.00 2.90
687 690 4.864704 TTTCAACAAGGTTAAGGGCATC 57.135 40.909 0.00 0.00 0.00 3.91
688 691 5.306678 TGATTTTCAACAAGGTTAAGGGCAT 59.693 36.000 0.00 0.00 0.00 4.40
689 692 4.651503 TGATTTTCAACAAGGTTAAGGGCA 59.348 37.500 0.00 0.00 0.00 5.36
690 693 5.208463 TGATTTTCAACAAGGTTAAGGGC 57.792 39.130 0.00 0.00 0.00 5.19
691 694 7.930865 TGATTTGATTTTCAACAAGGTTAAGGG 59.069 33.333 0.00 0.00 35.89 3.95
710 713 0.107017 GGCTGCTAGGGCTGATTTGA 60.107 55.000 0.00 0.00 39.31 2.69
729 732 3.473625 ACGTGGAGGGAGTAAGTTTTTG 58.526 45.455 0.00 0.00 0.00 2.44
805 809 3.201290 CGGTACAGTACTACTCCGTCAT 58.799 50.000 17.76 0.00 31.05 3.06
806 810 2.621338 CGGTACAGTACTACTCCGTCA 58.379 52.381 17.76 0.00 31.05 4.35
821 825 2.486951 ATGACACGTAGATGCGGTAC 57.513 50.000 0.00 0.00 35.98 3.34
834 838 9.662947 TTGATGATTAGATGGATGATATGACAC 57.337 33.333 0.00 0.00 0.00 3.67
842 846 6.236409 GCCTCTTTGATGATTAGATGGATGA 58.764 40.000 0.00 0.00 0.00 2.92
851 855 5.418840 GGTTTCTTGGCCTCTTTGATGATTA 59.581 40.000 3.32 0.00 0.00 1.75
857 861 2.746279 TGGTTTCTTGGCCTCTTTGA 57.254 45.000 3.32 0.00 0.00 2.69
952 959 1.071385 CACTTGCCCTCTGTGACTTCT 59.929 52.381 0.00 0.00 33.95 2.85
982 989 0.673644 ATCGCTTACTGCCGCTTGTT 60.674 50.000 0.00 0.00 38.78 2.83
1262 1269 3.003173 CCTTCACCTGGAGCCGGA 61.003 66.667 5.05 0.00 0.00 5.14
1311 1318 2.046314 CCGGCCACGAGGTTGATT 60.046 61.111 2.24 0.00 44.60 2.57
1681 1688 8.579850 TCTTGGACAAACATAGCAAATATCTT 57.420 30.769 0.00 0.00 0.00 2.40
1721 1728 8.463607 CCTAACAAAAGTAAAACTTGTCTTCCA 58.536 33.333 0.00 0.00 38.66 3.53
1750 1757 7.958567 CCAAATAATTGCACATGTTTTGTCATC 59.041 33.333 13.18 0.00 33.03 2.92
1771 1778 0.914644 TGCAGCTAGGCTCTCCAAAT 59.085 50.000 0.00 0.00 36.40 2.32
1969 1977 0.257039 AATCCCAAGCCTGCTAGGTG 59.743 55.000 7.72 0.00 37.80 4.00
2040 2048 3.134458 GTGAGCTATGATTGTGTAGCCC 58.866 50.000 0.00 0.00 43.32 5.19
2073 2081 4.811557 GGTGCATAGAAACAGGACTCATAC 59.188 45.833 0.00 0.00 0.00 2.39
2074 2082 4.716784 AGGTGCATAGAAACAGGACTCATA 59.283 41.667 0.00 0.00 0.00 2.15
2124 2134 8.421784 CCCTACATTCTTGTAACTCTTATGCTA 58.578 37.037 0.00 0.00 37.86 3.49
2125 2135 7.275920 CCCTACATTCTTGTAACTCTTATGCT 58.724 38.462 0.00 0.00 37.86 3.79
2511 2537 2.879756 GCCCCACGCCAATATCATACAT 60.880 50.000 0.00 0.00 0.00 2.29
2722 2748 4.329392 CTTTGGTACACCCCTCGTAAAAT 58.671 43.478 0.00 0.00 39.29 1.82
2879 2906 6.758886 TGGTAAACAGCAAAAACCAACAATAG 59.241 34.615 0.00 0.00 37.29 1.73
2919 2946 8.620416 GGCAAACATTCCAAGATTTTTAACTTT 58.380 29.630 0.00 0.00 0.00 2.66
2920 2947 7.772757 TGGCAAACATTCCAAGATTTTTAACTT 59.227 29.630 0.00 0.00 0.00 2.66
2921 2948 7.278875 TGGCAAACATTCCAAGATTTTTAACT 58.721 30.769 0.00 0.00 0.00 2.24
2922 2949 7.489574 TGGCAAACATTCCAAGATTTTTAAC 57.510 32.000 0.00 0.00 0.00 2.01
2923 2950 8.566260 CATTGGCAAACATTCCAAGATTTTTAA 58.434 29.630 3.01 0.00 44.59 1.52
2924 2951 7.718753 ACATTGGCAAACATTCCAAGATTTTTA 59.281 29.630 3.01 0.00 44.59 1.52
2925 2952 6.546772 ACATTGGCAAACATTCCAAGATTTTT 59.453 30.769 3.01 0.00 44.59 1.94
2926 2953 6.063404 ACATTGGCAAACATTCCAAGATTTT 58.937 32.000 3.01 0.00 44.59 1.82
2927 2954 5.623169 ACATTGGCAAACATTCCAAGATTT 58.377 33.333 3.01 0.00 44.59 2.17
2928 2955 5.231702 ACATTGGCAAACATTCCAAGATT 57.768 34.783 3.01 0.00 44.59 2.40
2929 2956 4.895668 ACATTGGCAAACATTCCAAGAT 57.104 36.364 3.01 0.00 44.59 2.40
2930 2957 4.686191 AACATTGGCAAACATTCCAAGA 57.314 36.364 3.01 0.00 44.59 3.02
2931 2958 4.575645 ACAAACATTGGCAAACATTCCAAG 59.424 37.500 3.01 0.00 44.59 3.61
2932 2959 4.521146 ACAAACATTGGCAAACATTCCAA 58.479 34.783 3.01 0.00 45.35 3.53
2933 2960 4.148128 ACAAACATTGGCAAACATTCCA 57.852 36.364 3.01 0.00 34.12 3.53
2934 2961 4.574013 TGAACAAACATTGGCAAACATTCC 59.426 37.500 3.01 0.00 34.12 3.01
2935 2962 5.523188 TCTGAACAAACATTGGCAAACATTC 59.477 36.000 3.01 3.81 34.12 2.67
2936 2963 5.426504 TCTGAACAAACATTGGCAAACATT 58.573 33.333 3.01 0.00 34.12 2.71
3056 3083 1.064685 ACCAGGCCAAGGTAATACAGC 60.065 52.381 17.47 0.00 37.67 4.40
3215 3259 0.251430 TGGGGGAACAAAATCCGTCC 60.251 55.000 0.00 0.00 40.62 4.79
3248 3292 4.280929 ACATGTATCGGCAGAATAGTAGCA 59.719 41.667 0.00 0.00 0.00 3.49
3263 3307 8.979574 GCATTTCTACTAAGGTACACATGTATC 58.020 37.037 0.00 0.00 32.54 2.24
3326 3370 6.388619 ACCTAAACCAATGGAACTAGTGAT 57.611 37.500 6.16 0.00 0.00 3.06
3388 3432 2.728690 ACGCAACACTATAACCGACA 57.271 45.000 0.00 0.00 0.00 4.35
3389 3433 2.988493 TCAACGCAACACTATAACCGAC 59.012 45.455 0.00 0.00 0.00 4.79
3426 3470 1.345089 TGTTACTTCTGCCCACGCTTA 59.655 47.619 0.00 0.00 35.36 3.09
3485 3532 7.654520 ACTGTATCACGTTTAGTTGTGTGTATT 59.345 33.333 0.00 0.00 37.38 1.89
3516 3563 3.854784 GCTGCTGGATTGAACTTTGACAC 60.855 47.826 0.00 0.00 0.00 3.67
3575 3622 4.789697 GCAGATGCAAACTCATCCTGAGG 61.790 52.174 8.85 0.00 43.90 3.86
3576 3623 2.355132 GCAGATGCAAACTCATCCTGAG 59.645 50.000 0.00 2.65 44.56 3.35
3577 3624 2.362736 GCAGATGCAAACTCATCCTGA 58.637 47.619 0.00 0.00 42.84 3.86
3774 3824 8.667987 TCGCAATAAATCAGAACAAACATTAC 57.332 30.769 0.00 0.00 0.00 1.89
4708 4758 3.747529 GCATCAACCATTCCACCAAAAAG 59.252 43.478 0.00 0.00 0.00 2.27
5065 5115 1.065928 CCCGCTCTACATCACCGTC 59.934 63.158 0.00 0.00 0.00 4.79
5181 5231 9.330063 GAAGTCATCACAAGTAATATGGATCAA 57.670 33.333 0.00 0.00 0.00 2.57
5215 5268 6.094048 GCATACTAATCCTTCTTTTCACAGCA 59.906 38.462 0.00 0.00 0.00 4.41
5258 5366 2.622942 TGTCCAGGATGAAAAACTGCAC 59.377 45.455 0.00 0.00 39.69 4.57
5264 5372 6.462768 CCACAATTTCTGTCCAGGATGAAAAA 60.463 38.462 18.62 7.76 34.61 1.94
5401 5509 6.544038 AGCAACACAAGCCAATTTTAAATC 57.456 33.333 0.00 0.00 0.00 2.17
5444 5552 9.810545 TTTAACACCAAAAGTTTCAAATCCTAG 57.189 29.630 0.00 0.00 0.00 3.02
5481 5589 6.892456 GGAAAGTCCTTTTATTCCCTCTCAAT 59.108 38.462 0.00 0.00 36.21 2.57
5483 5591 5.816682 GGAAAGTCCTTTTATTCCCTCTCA 58.183 41.667 0.00 0.00 36.21 3.27
5640 5748 3.960102 AGGAAGTCATGTCATCCTCTCTC 59.040 47.826 10.41 0.00 37.80 3.20
5641 5749 3.992999 AGGAAGTCATGTCATCCTCTCT 58.007 45.455 10.41 0.00 37.80 3.10
5769 5878 7.712264 TTAAATCATTGCCAACTCTTTTGTG 57.288 32.000 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.