Multiple sequence alignment - TraesCS2A01G455000

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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 TraesCS2A01G455000 chr2A 100.000 4352 0 0 1 4352 703864739 703869090 0.000000e+00 8037.0
1 TraesCS2A01G455000 chr2A 91.935 62 5 0 646 707 24367942 24368003 2.160000e-13 87.9
2 TraesCS2A01G455000 chr2D 94.163 3632 129 37 779 4352 563783223 563786829 0.000000e+00 5456.0
3 TraesCS2A01G455000 chr2D 89.394 66 7 0 642 707 69254220 69254285 2.790000e-12 84.2
4 TraesCS2A01G455000 chr2B 94.381 3257 140 25 779 4006 674026619 674029861 0.000000e+00 4961.0
5 TraesCS2A01G455000 chr2B 88.352 352 16 10 4002 4352 674029903 674030230 2.440000e-107 399.0
6 TraesCS2A01G455000 chr2B 92.308 65 5 0 643 707 148251681 148251745 4.630000e-15 93.5
7 TraesCS2A01G455000 chr2B 90.909 66 6 0 642 707 636104644 636104709 5.990000e-14 89.8
8 TraesCS2A01G455000 chr4A 93.385 650 37 3 1 645 655163311 655163959 0.000000e+00 957.0
9 TraesCS2A01G455000 chr4A 93.939 66 3 1 709 773 655164341 655164406 9.960000e-17 99.0
10 TraesCS2A01G455000 chr4A 93.750 64 3 1 709 771 63013977 63014040 1.290000e-15 95.3
11 TraesCS2A01G455000 chr7B 93.231 650 38 3 1 645 246379258 246379906 0.000000e+00 952.0
12 TraesCS2A01G455000 chr7B 93.231 650 38 3 1 645 656512856 656512208 0.000000e+00 952.0
13 TraesCS2A01G455000 chr7B 90.851 623 36 5 24 641 604360136 604359530 0.000000e+00 815.0
14 TraesCS2A01G455000 chr7B 93.750 64 3 1 711 773 246380290 246380353 1.290000e-15 95.3
15 TraesCS2A01G455000 chr7B 93.750 64 3 1 709 771 604359151 604359088 1.290000e-15 95.3
16 TraesCS2A01G455000 chr7B 93.750 64 3 1 709 771 656511826 656511763 1.290000e-15 95.3
17 TraesCS2A01G455000 chr6B 93.045 647 39 3 4 645 652757408 652756763 0.000000e+00 941.0
18 TraesCS2A01G455000 chr1A 90.312 609 43 8 43 644 66052486 66053085 0.000000e+00 784.0
19 TraesCS2A01G455000 chr1A 84.332 217 26 4 1707 1922 524117645 524117854 5.710000e-49 206.0
20 TraesCS2A01G455000 chr1A 83.871 217 27 5 1707 1922 525912083 525912292 2.650000e-47 200.0
21 TraesCS2A01G455000 chr1A 96.721 61 1 1 709 768 66053465 66053525 2.770000e-17 100.0
22 TraesCS2A01G455000 chr4B 91.771 559 40 3 91 644 663881192 663880635 0.000000e+00 773.0
23 TraesCS2A01G455000 chr4B 93.939 66 3 1 709 773 650727962 650728027 9.960000e-17 99.0
24 TraesCS2A01G455000 chr6A 92.488 426 26 3 2 423 580000109 579999686 4.810000e-169 604.0
25 TraesCS2A01G455000 chr6A 92.544 228 16 1 419 645 579992539 579992312 4.200000e-85 326.0
26 TraesCS2A01G455000 chr3A 93.842 341 20 1 306 645 745272017 745271677 3.000000e-141 512.0
27 TraesCS2A01G455000 chr1B 93.939 66 3 1 709 773 413206726 413206661 9.960000e-17 99.0
28 TraesCS2A01G455000 chr5A 93.750 64 3 1 709 771 672756231 672756294 1.290000e-15 95.3
29 TraesCS2A01G455000 chr5D 90.769 65 6 0 643 707 428684668 428684732 2.160000e-13 87.9
30 TraesCS2A01G455000 chr3D 90.625 64 6 0 644 707 32009779 32009842 7.750000e-13 86.1
31 TraesCS2A01G455000 chr7D 89.394 66 7 0 642 707 42795258 42795193 2.790000e-12 84.2
32 TraesCS2A01G455000 chr3B 89.394 66 7 0 642 707 384727466 384727401 2.790000e-12 84.2
33 TraesCS2A01G455000 chr4D 90.323 62 6 0 644 705 348795054 348794993 1.000000e-11 82.4


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 TraesCS2A01G455000 chr2A 703864739 703869090 4351 False 8037.00 8037 100.0000 1 4352 1 chr2A.!!$F2 4351
1 TraesCS2A01G455000 chr2D 563783223 563786829 3606 False 5456.00 5456 94.1630 779 4352 1 chr2D.!!$F2 3573
2 TraesCS2A01G455000 chr2B 674026619 674030230 3611 False 2680.00 4961 91.3665 779 4352 2 chr2B.!!$F3 3573
3 TraesCS2A01G455000 chr4A 655163311 655164406 1095 False 528.00 957 93.6620 1 773 2 chr4A.!!$F2 772
4 TraesCS2A01G455000 chr7B 246379258 246380353 1095 False 523.65 952 93.4905 1 773 2 chr7B.!!$F1 772
5 TraesCS2A01G455000 chr7B 656511763 656512856 1093 True 523.65 952 93.4905 1 771 2 chr7B.!!$R2 770
6 TraesCS2A01G455000 chr7B 604359088 604360136 1048 True 455.15 815 92.3005 24 771 2 chr7B.!!$R1 747
7 TraesCS2A01G455000 chr6B 652756763 652757408 645 True 941.00 941 93.0450 4 645 1 chr6B.!!$R1 641
8 TraesCS2A01G455000 chr1A 66052486 66053525 1039 False 442.00 784 93.5165 43 768 2 chr1A.!!$F3 725
9 TraesCS2A01G455000 chr4B 663880635 663881192 557 True 773.00 773 91.7710 91 644 1 chr4B.!!$R1 553

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
643 653 0.107268 CGATGCATCAGTCCATGGGA 59.893 55.0 25.7 1.1 0.00 4.37 F
1286 1642 0.623723 TCCAGTCCCCAGTATTTGGC 59.376 55.0 0.0 0.0 46.32 4.52 F
1574 1930 0.765510 AGTTCTGTCCACTTGGTCCC 59.234 55.0 0.0 0.0 36.34 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1540 1896 1.000396 AACTGCTCCATCCCAAGGC 60.000 57.895 0.00 0.00 0.0 4.35 R
3260 3669 0.390340 TGCCGACTAGAAAGCTGCAG 60.390 55.000 10.11 10.11 0.0 4.41 R
3528 3938 1.683917 AGAGGTCAGCACATATCCGAC 59.316 52.381 0.00 0.00 0.0 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
30 31 0.249447 CTGTCCGCTCGGCATATCAA 60.249 55.000 2.96 0.00 34.68 2.57
53 54 5.624159 AGTGGAGTTTGATCATCAGTTTGA 58.376 37.500 0.00 0.00 0.00 2.69
132 134 3.289834 CTGTGGCAACTGCGGCTT 61.290 61.111 0.00 0.00 43.26 4.35
176 178 2.561419 GTTGAAAAGTCCTAAAGGGGGC 59.439 50.000 0.00 0.00 35.41 5.80
212 218 1.070758 CGTTCTGGCAGGCATATACCT 59.929 52.381 15.73 0.00 42.30 3.08
295 301 2.358615 GCGCATGGGCATCCGATA 60.359 61.111 28.03 0.00 41.24 2.92
359 365 0.933097 CGGCAAGATCGATCTGGTTG 59.067 55.000 27.93 22.09 37.19 3.77
389 397 0.810648 GAAATTCTGGTCCGCATGCA 59.189 50.000 19.57 0.00 0.00 3.96
429 437 1.734465 CCAACGGCTGAACTCATCTTC 59.266 52.381 0.00 0.00 0.00 2.87
448 456 4.693566 TCTTCGTTGTGATGTGGTTTATCC 59.306 41.667 0.00 0.00 0.00 2.59
476 484 2.500098 AGAGGCGCCAAGTAACTAATGA 59.500 45.455 31.54 0.00 0.00 2.57
536 546 1.804748 CCGAGTTTTAGCCACCAACTC 59.195 52.381 0.00 0.00 42.02 3.01
561 571 2.224426 ACGAGCCTACACACCAAATCAA 60.224 45.455 0.00 0.00 0.00 2.57
569 579 2.222886 CACACCAAATCAACCGGTACA 58.777 47.619 8.00 0.00 0.00 2.90
599 609 1.093159 CATCAGTGGAAGAAGCCAGC 58.907 55.000 0.00 0.00 38.95 4.85
630 640 4.436317 GCGGTAAAAGTTAATGTCGATGCA 60.436 41.667 0.00 0.00 0.00 3.96
634 644 6.907212 GGTAAAAGTTAATGTCGATGCATCAG 59.093 38.462 25.70 17.71 0.00 2.90
641 651 1.224075 GTCGATGCATCAGTCCATGG 58.776 55.000 25.70 4.97 0.00 3.66
643 653 0.107268 CGATGCATCAGTCCATGGGA 59.893 55.000 25.70 1.10 0.00 4.37
654 664 2.584835 TCCATGGGACTTGAAACCTG 57.415 50.000 13.02 0.00 0.00 4.00
656 666 1.203050 CCATGGGACTTGAAACCTGGT 60.203 52.381 2.85 0.00 0.00 4.00
657 667 1.888512 CATGGGACTTGAAACCTGGTG 59.111 52.381 0.00 0.00 0.00 4.17
669 679 2.579410 ACCTGGTGGTTTGTGGATAC 57.421 50.000 0.00 0.00 46.05 2.24
670 680 1.074889 ACCTGGTGGTTTGTGGATACC 59.925 52.381 0.00 0.00 46.05 2.73
671 681 1.074727 CCTGGTGGTTTGTGGATACCA 59.925 52.381 0.00 0.00 41.97 3.25
684 694 3.371965 TGGATACCACTGTCCCTCTAAC 58.628 50.000 0.00 0.00 33.45 2.34
687 697 2.344093 ACCACTGTCCCTCTAACCAT 57.656 50.000 0.00 0.00 0.00 3.55
688 698 2.632537 ACCACTGTCCCTCTAACCATT 58.367 47.619 0.00 0.00 0.00 3.16
689 699 2.572104 ACCACTGTCCCTCTAACCATTC 59.428 50.000 0.00 0.00 0.00 2.67
690 700 2.571653 CCACTGTCCCTCTAACCATTCA 59.428 50.000 0.00 0.00 0.00 2.57
692 702 4.324563 CCACTGTCCCTCTAACCATTCAAT 60.325 45.833 0.00 0.00 0.00 2.57
693 703 4.878397 CACTGTCCCTCTAACCATTCAATC 59.122 45.833 0.00 0.00 0.00 2.67
694 704 4.536090 ACTGTCCCTCTAACCATTCAATCA 59.464 41.667 0.00 0.00 0.00 2.57
695 705 4.843728 TGTCCCTCTAACCATTCAATCAC 58.156 43.478 0.00 0.00 0.00 3.06
696 706 4.288366 TGTCCCTCTAACCATTCAATCACA 59.712 41.667 0.00 0.00 0.00 3.58
697 707 4.878397 GTCCCTCTAACCATTCAATCACAG 59.122 45.833 0.00 0.00 0.00 3.66
698 708 4.080356 TCCCTCTAACCATTCAATCACAGG 60.080 45.833 0.00 0.00 0.00 4.00
699 709 4.324563 CCCTCTAACCATTCAATCACAGGT 60.325 45.833 0.00 0.00 0.00 4.00
700 710 5.256474 CCTCTAACCATTCAATCACAGGTT 58.744 41.667 0.00 0.00 44.23 3.50
701 711 5.124457 CCTCTAACCATTCAATCACAGGTTG 59.876 44.000 0.00 0.00 42.19 3.77
702 712 5.009631 TCTAACCATTCAATCACAGGTTGG 58.990 41.667 0.00 0.00 42.19 3.77
703 713 3.243359 ACCATTCAATCACAGGTTGGT 57.757 42.857 0.00 0.00 0.00 3.67
704 714 3.575805 ACCATTCAATCACAGGTTGGTT 58.424 40.909 0.00 0.00 32.23 3.67
705 715 3.573967 ACCATTCAATCACAGGTTGGTTC 59.426 43.478 0.00 0.00 32.23 3.62
706 716 3.366273 CCATTCAATCACAGGTTGGTTCG 60.366 47.826 0.00 0.00 0.00 3.95
707 717 2.631160 TCAATCACAGGTTGGTTCGT 57.369 45.000 0.00 0.00 0.00 3.85
727 1064 7.746475 GGTTCGTGACTTTATTCTTCATTCTTG 59.254 37.037 0.00 0.00 0.00 3.02
802 1140 2.890808 TTCTGCCGAATAAGCGAGAT 57.109 45.000 0.00 0.00 0.00 2.75
831 1169 2.557924 TCAGAATCCAAGCAAACGCATT 59.442 40.909 0.00 0.00 0.00 3.56
951 1290 1.336887 CGTCCTTGTACCAGTGTCCAG 60.337 57.143 0.00 0.00 0.00 3.86
975 1314 3.431725 GCTGCGGCAACTACCCAC 61.432 66.667 14.08 0.00 38.54 4.61
1008 1359 2.413963 CCATTCCGGCATGGCGAAA 61.414 57.895 39.49 29.49 37.51 3.46
1267 1621 2.370445 CCGCCTCATCCCTCTTGGT 61.370 63.158 0.00 0.00 34.77 3.67
1286 1642 0.623723 TCCAGTCCCCAGTATTTGGC 59.376 55.000 0.00 0.00 46.32 4.52
1413 1769 5.827797 TGTTTGACTTGGATTATGCTATCCC 59.172 40.000 9.58 0.00 42.91 3.85
1414 1770 5.645056 TTGACTTGGATTATGCTATCCCA 57.355 39.130 9.58 0.00 42.91 4.37
1457 1813 5.324784 ACGAGAGTTGTCAGTGCATAATA 57.675 39.130 0.00 0.00 46.40 0.98
1524 1880 0.937304 GTTGCGTCATCTGTGTGTGT 59.063 50.000 0.00 0.00 0.00 3.72
1525 1881 0.936600 TTGCGTCATCTGTGTGTGTG 59.063 50.000 0.00 0.00 0.00 3.82
1540 1896 3.631686 TGTGTGTGGTCTTGGAGAATTTG 59.368 43.478 0.00 0.00 0.00 2.32
1567 1923 1.277557 GATGGAGCAGTTCTGTCCACT 59.722 52.381 18.64 12.02 43.18 4.00
1568 1924 1.131638 TGGAGCAGTTCTGTCCACTT 58.868 50.000 14.98 0.00 35.36 3.16
1569 1925 1.202687 TGGAGCAGTTCTGTCCACTTG 60.203 52.381 14.98 0.00 35.36 3.16
1570 1926 1.517242 GAGCAGTTCTGTCCACTTGG 58.483 55.000 1.78 0.00 0.00 3.61
1571 1927 0.839946 AGCAGTTCTGTCCACTTGGT 59.160 50.000 1.78 0.00 36.34 3.67
1572 1928 1.202698 AGCAGTTCTGTCCACTTGGTC 60.203 52.381 1.78 0.00 36.34 4.02
1573 1929 1.884235 CAGTTCTGTCCACTTGGTCC 58.116 55.000 0.00 0.00 36.34 4.46
1574 1930 0.765510 AGTTCTGTCCACTTGGTCCC 59.234 55.000 0.00 0.00 36.34 4.46
1575 1931 0.765510 GTTCTGTCCACTTGGTCCCT 59.234 55.000 0.00 0.00 36.34 4.20
1660 2034 6.173339 ACTTCTGAGTCACTTTCACTGAAAA 58.827 36.000 5.72 0.00 30.84 2.29
1698 2077 8.370940 TCTATCTTGGGATGACATTATCTTGTC 58.629 37.037 0.00 0.00 45.05 3.18
1711 2090 6.260936 ACATTATCTTGTCGATAGCTTTTGGG 59.739 38.462 0.00 0.00 36.06 4.12
1719 2098 1.671328 GATAGCTTTTGGGACTTCGCC 59.329 52.381 0.00 0.00 0.00 5.54
1839 2244 7.445402 ACTTCAGAAACAACATAGTAGTGCATT 59.555 33.333 0.00 0.00 0.00 3.56
1840 2245 8.840833 TTCAGAAACAACATAGTAGTGCATTA 57.159 30.769 0.00 0.00 0.00 1.90
2046 2451 6.946009 ACCTTGAGTTTTATTTTAGCTGCCTA 59.054 34.615 0.00 0.00 0.00 3.93
2404 2813 2.346803 GGATGCGTACAGACAATGTGT 58.653 47.619 0.00 0.00 43.80 3.72
2505 2914 5.059833 GGTATCTGGAGATGATGTGGAAAC 58.940 45.833 0.00 0.00 36.05 2.78
2575 2984 8.969267 CATATTCTCGGTAAATTACTCAGTCAC 58.031 37.037 2.96 0.00 0.00 3.67
2624 3033 1.559368 CCTTGTTGCCCATGATGGAA 58.441 50.000 14.26 0.00 40.96 3.53
2635 3044 5.128919 GCCCATGATGGAATATAGTGATCC 58.871 45.833 14.26 0.00 40.96 3.36
2640 3049 9.305555 CCATGATGGAATATAGTGATCCTTTTT 57.694 33.333 5.27 0.00 40.96 1.94
2676 3085 6.543831 ACATGCTTATCAGGTTTAGTTCATCC 59.456 38.462 0.00 0.00 36.06 3.51
2787 3196 1.156736 GCTTGCGACCACTATGTTGT 58.843 50.000 0.00 0.00 0.00 3.32
3004 3413 2.446435 ACAGCATACTTTGGCGGATTT 58.554 42.857 0.00 0.00 34.54 2.17
3111 3520 6.776744 TGAGGATTATGATGGAAGATTGGAG 58.223 40.000 0.00 0.00 0.00 3.86
3197 3606 7.765360 CACAAAATTGCAGGTATTATGTCCAAT 59.235 33.333 0.00 0.00 0.00 3.16
3239 3648 7.786178 TTTAGTAAGAAATGTGATCGGATGG 57.214 36.000 0.00 0.00 0.00 3.51
3260 3669 4.226761 GGAATTTTGTCGGTTCATGTGTC 58.773 43.478 0.00 0.00 0.00 3.67
3295 3704 4.082787 AGTCGGCATATTTTTGTTCTGGTG 60.083 41.667 0.00 0.00 0.00 4.17
3578 3988 7.451255 TGGATGAAACATAACTTCCTTGAATGT 59.549 33.333 0.00 0.00 33.41 2.71
3631 4045 1.413445 GCCTGCTGAGATGAGAGACAT 59.587 52.381 0.00 0.00 42.47 3.06
3671 4086 5.692654 TCGTTTTTCTGTGTATTGTCATCGA 59.307 36.000 0.00 0.00 0.00 3.59
3751 4168 4.148825 CTTCCCGGCGACCCTCAG 62.149 72.222 9.30 0.00 0.00 3.35
3946 4364 9.787532 TTCTTAGCAAAATTACATTCTGCATAC 57.212 29.630 0.00 0.00 35.44 2.39
3996 4415 0.542805 GCCCATACTGGACCGGTTTA 59.457 55.000 12.24 0.00 40.96 2.01
4073 4542 4.907875 AGCTCTGTAATATTGGGCTTCCTA 59.092 41.667 0.00 0.00 0.00 2.94
4085 4554 0.530870 GCTTCCTAGCACGGTCCATC 60.531 60.000 0.00 0.00 46.95 3.51
4090 4559 2.650813 CTAGCACGGTCCATCCAGCC 62.651 65.000 0.00 0.00 37.52 4.85
4095 4564 2.668632 GGTCCATCCAGCCGAACA 59.331 61.111 0.00 0.00 35.97 3.18
4144 4615 2.260869 CCCTCGGCCTTGTTGTGTG 61.261 63.158 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 5.624159 TCAAACTGATGATCAAACTCCACT 58.376 37.500 0.00 0.00 0.00 4.00
53 54 6.034683 GCTATTCGAGTTTGAGTAATGACGTT 59.965 38.462 0.00 0.00 0.00 3.99
132 134 5.059833 CCAAAATGTTTGATTTTTCCCGGA 58.940 37.500 0.73 0.00 0.00 5.14
159 161 1.467969 AGGCCCCCTTTAGGACTTTT 58.532 50.000 0.00 0.00 41.26 2.27
212 218 0.671251 GCGGACATTGTGGAACCAAA 59.329 50.000 0.00 0.00 34.36 3.28
273 279 2.894879 GATGCCCATGCGCGTGTA 60.895 61.111 26.86 13.93 41.78 2.90
283 289 1.774254 AGACCAAATATCGGATGCCCA 59.226 47.619 0.00 0.00 0.00 5.36
295 301 4.922206 TGCAATCCTAACTCAGACCAAAT 58.078 39.130 0.00 0.00 0.00 2.32
359 365 6.677187 GCGGACCAGAATTTCCAAAGTTATAC 60.677 42.308 0.00 0.00 0.00 1.47
389 397 3.181437 TGGCAGCTCATGAATCATGGTAT 60.181 43.478 21.58 6.32 41.66 2.73
429 437 2.095213 CCGGATAAACCACATCACAACG 59.905 50.000 0.00 0.00 38.90 4.10
476 484 0.896019 CGGTGTCTGGACTGACTCCT 60.896 60.000 20.51 0.00 44.11 3.69
536 546 1.138247 GGTGTGTAGGCTCGTACGG 59.862 63.158 16.52 7.41 0.00 4.02
561 571 2.646930 TGACTGATCGTATGTACCGGT 58.353 47.619 13.98 13.98 0.00 5.28
569 579 4.889995 TCTTCCACTGATGACTGATCGTAT 59.110 41.667 0.00 0.00 33.17 3.06
599 609 0.036671 AACTTTTACCGCTCCCTCCG 60.037 55.000 0.00 0.00 0.00 4.63
651 661 1.074727 TGGTATCCACAAACCACCAGG 59.925 52.381 0.00 0.00 40.84 4.45
652 662 2.577606 TGGTATCCACAAACCACCAG 57.422 50.000 0.00 0.00 40.84 4.00
663 673 3.371965 GTTAGAGGGACAGTGGTATCCA 58.628 50.000 0.00 0.00 36.65 3.41
666 676 3.484953 TGGTTAGAGGGACAGTGGTAT 57.515 47.619 0.00 0.00 0.00 2.73
667 677 3.484953 ATGGTTAGAGGGACAGTGGTA 57.515 47.619 0.00 0.00 0.00 3.25
668 678 2.344093 ATGGTTAGAGGGACAGTGGT 57.656 50.000 0.00 0.00 0.00 4.16
669 679 2.571653 TGAATGGTTAGAGGGACAGTGG 59.428 50.000 0.00 0.00 0.00 4.00
670 680 3.981071 TGAATGGTTAGAGGGACAGTG 57.019 47.619 0.00 0.00 0.00 3.66
671 681 4.536090 TGATTGAATGGTTAGAGGGACAGT 59.464 41.667 0.00 0.00 0.00 3.55
672 682 4.878397 GTGATTGAATGGTTAGAGGGACAG 59.122 45.833 0.00 0.00 0.00 3.51
673 683 4.288366 TGTGATTGAATGGTTAGAGGGACA 59.712 41.667 0.00 0.00 0.00 4.02
674 684 4.843728 TGTGATTGAATGGTTAGAGGGAC 58.156 43.478 0.00 0.00 0.00 4.46
677 687 4.848357 ACCTGTGATTGAATGGTTAGAGG 58.152 43.478 0.00 0.00 0.00 3.69
678 688 5.124457 CCAACCTGTGATTGAATGGTTAGAG 59.876 44.000 0.00 0.00 38.76 2.43
679 689 5.009631 CCAACCTGTGATTGAATGGTTAGA 58.990 41.667 0.00 0.00 38.76 2.10
680 690 4.766891 ACCAACCTGTGATTGAATGGTTAG 59.233 41.667 0.00 0.00 38.76 2.34
682 692 3.575805 ACCAACCTGTGATTGAATGGTT 58.424 40.909 0.00 0.00 41.12 3.67
684 694 3.366273 CGAACCAACCTGTGATTGAATGG 60.366 47.826 0.00 0.00 0.00 3.16
687 697 2.616376 CACGAACCAACCTGTGATTGAA 59.384 45.455 0.00 0.00 34.29 2.69
688 698 2.158885 TCACGAACCAACCTGTGATTGA 60.159 45.455 0.00 0.00 36.50 2.57
689 699 2.032030 GTCACGAACCAACCTGTGATTG 60.032 50.000 0.00 0.00 42.66 2.67
690 700 2.158813 AGTCACGAACCAACCTGTGATT 60.159 45.455 0.00 0.00 42.66 2.57
692 702 0.828022 AGTCACGAACCAACCTGTGA 59.172 50.000 0.00 0.00 38.91 3.58
693 703 1.663695 AAGTCACGAACCAACCTGTG 58.336 50.000 0.00 0.00 0.00 3.66
694 704 2.413310 AAAGTCACGAACCAACCTGT 57.587 45.000 0.00 0.00 0.00 4.00
695 705 4.755123 AGAATAAAGTCACGAACCAACCTG 59.245 41.667 0.00 0.00 0.00 4.00
696 706 4.969484 AGAATAAAGTCACGAACCAACCT 58.031 39.130 0.00 0.00 0.00 3.50
697 707 5.237779 TGAAGAATAAAGTCACGAACCAACC 59.762 40.000 0.00 0.00 0.00 3.77
698 708 6.295039 TGAAGAATAAAGTCACGAACCAAC 57.705 37.500 0.00 0.00 0.00 3.77
699 709 7.444183 AGAATGAAGAATAAAGTCACGAACCAA 59.556 33.333 0.00 0.00 0.00 3.67
700 710 6.934645 AGAATGAAGAATAAAGTCACGAACCA 59.065 34.615 0.00 0.00 0.00 3.67
701 711 7.365840 AGAATGAAGAATAAAGTCACGAACC 57.634 36.000 0.00 0.00 0.00 3.62
702 712 8.283291 ACAAGAATGAAGAATAAAGTCACGAAC 58.717 33.333 0.00 0.00 0.00 3.95
703 713 8.282592 CACAAGAATGAAGAATAAAGTCACGAA 58.717 33.333 0.00 0.00 0.00 3.85
704 714 7.441157 ACACAAGAATGAAGAATAAAGTCACGA 59.559 33.333 0.00 0.00 0.00 4.35
705 715 7.576236 ACACAAGAATGAAGAATAAAGTCACG 58.424 34.615 0.00 0.00 0.00 4.35
727 1064 7.290857 TCAAATAAGAGCAAGATCGTTACAC 57.709 36.000 0.00 0.00 0.00 2.90
776 1114 6.092944 TCTCGCTTATTCGGCAGAATTAAAAA 59.907 34.615 17.30 5.04 44.11 1.94
777 1115 5.583061 TCTCGCTTATTCGGCAGAATTAAAA 59.417 36.000 17.30 5.38 44.11 1.52
796 1134 2.015736 TTCTGAGCCTTTGATCTCGC 57.984 50.000 0.00 0.00 32.20 5.03
802 1140 2.224843 TGCTTGGATTCTGAGCCTTTGA 60.225 45.455 8.59 0.00 35.59 2.69
874 1212 2.993899 CGATGTAGTTTGAAAGCGGAGT 59.006 45.455 0.00 0.00 0.00 3.85
875 1213 2.348666 CCGATGTAGTTTGAAAGCGGAG 59.651 50.000 0.00 0.00 39.85 4.63
936 1275 1.070134 GCAGACTGGACACTGGTACAA 59.930 52.381 4.26 0.00 37.42 2.41
1267 1621 0.623723 GCCAAATACTGGGGACTGGA 59.376 55.000 0.00 0.00 46.54 3.86
1413 1769 5.516696 CGTTTAGAGTACATCACTGGACATG 59.483 44.000 0.00 0.00 38.84 3.21
1414 1770 5.417894 TCGTTTAGAGTACATCACTGGACAT 59.582 40.000 0.00 0.00 38.84 3.06
1524 1880 2.892852 CAAGGCAAATTCTCCAAGACCA 59.107 45.455 0.00 0.00 0.00 4.02
1525 1881 2.232208 CCAAGGCAAATTCTCCAAGACC 59.768 50.000 0.00 0.00 0.00 3.85
1540 1896 1.000396 AACTGCTCCATCCCAAGGC 60.000 57.895 0.00 0.00 0.00 4.35
1571 1927 2.496070 CACATCTAAGACGTCCAAGGGA 59.504 50.000 13.01 4.44 0.00 4.20
1572 1928 2.496070 TCACATCTAAGACGTCCAAGGG 59.504 50.000 13.01 8.52 0.00 3.95
1573 1929 3.868757 TCACATCTAAGACGTCCAAGG 57.131 47.619 13.01 0.38 0.00 3.61
1574 1930 6.378710 TCTATCACATCTAAGACGTCCAAG 57.621 41.667 13.01 10.18 0.00 3.61
1575 1931 6.961360 ATCTATCACATCTAAGACGTCCAA 57.039 37.500 13.01 0.00 0.00 3.53
1660 2034 7.674348 TCATCCCAAGATAGATACTAATTCGGT 59.326 37.037 0.00 0.00 0.00 4.69
1692 2071 3.260884 AGTCCCAAAAGCTATCGACAAGA 59.739 43.478 0.86 0.00 0.00 3.02
1698 2077 1.327764 GCGAAGTCCCAAAAGCTATCG 59.672 52.381 0.00 0.00 0.00 2.92
1839 2244 6.032094 GCGAAACTAAGTGCTAGTGTGTATA 58.968 40.000 0.00 0.00 40.14 1.47
1840 2245 4.863131 GCGAAACTAAGTGCTAGTGTGTAT 59.137 41.667 0.00 0.00 40.14 2.29
1933 2338 4.215827 ACTCCTATTACGTGAATAGCCTCG 59.784 45.833 0.00 0.00 44.02 4.63
1971 2376 2.693797 AAACATCGCTGTTGCTTCTG 57.306 45.000 5.25 0.00 44.83 3.02
2404 2813 4.574674 AAGCAATAGTGGTGGATCTTGA 57.425 40.909 0.00 0.00 35.09 3.02
2505 2914 1.590238 CAGCCGCAAGAAATCTAGTCG 59.410 52.381 0.00 0.00 43.02 4.18
2635 3044 8.807667 ATAAGCATGTTTCACAGAAGAAAAAG 57.192 30.769 0.00 0.00 39.05 2.27
2640 3049 5.645067 CCTGATAAGCATGTTTCACAGAAGA 59.355 40.000 21.09 0.00 0.00 2.87
2654 3063 6.061022 TGGATGAACTAAACCTGATAAGCA 57.939 37.500 0.00 0.00 0.00 3.91
2659 3068 7.405292 TGAAAGATGGATGAACTAAACCTGAT 58.595 34.615 0.00 0.00 0.00 2.90
2787 3196 4.639755 TGTTTCTCAAGTCTGTTGCATTCA 59.360 37.500 0.00 0.00 0.00 2.57
3004 3413 6.707440 TTTAAATCTCTGCTTGGTTCACAA 57.293 33.333 0.00 0.00 37.55 3.33
3088 3497 6.013032 TCCTCCAATCTTCCATCATAATCCTC 60.013 42.308 0.00 0.00 0.00 3.71
3111 3520 3.010420 GGAGGCAGTGACAAATAGTTCC 58.990 50.000 0.00 0.00 0.00 3.62
3197 3606 6.140303 ACTAAAACAGTCTTCACGTCACTA 57.860 37.500 0.00 0.00 28.33 2.74
3233 3642 2.486203 TGAACCGACAAAATTCCATCCG 59.514 45.455 0.00 0.00 0.00 4.18
3239 3648 4.911610 CAGACACATGAACCGACAAAATTC 59.088 41.667 0.00 0.00 0.00 2.17
3260 3669 0.390340 TGCCGACTAGAAAGCTGCAG 60.390 55.000 10.11 10.11 0.00 4.41
3295 3704 9.369904 ACAATTAAAATGATTAGATGCAACACC 57.630 29.630 0.00 0.00 0.00 4.16
3327 3736 1.890876 TTAGCGAAGAAAGGCTGCAA 58.109 45.000 0.50 0.00 40.32 4.08
3528 3938 1.683917 AGAGGTCAGCACATATCCGAC 59.316 52.381 0.00 0.00 0.00 4.79
3686 4102 6.538381 TGAGAAGCGCATATACATCTTTTCAA 59.462 34.615 11.47 0.00 28.99 2.69
3751 4168 8.515414 AGTTCAAAATAGGAAAGTAACTGCATC 58.485 33.333 0.00 0.00 0.00 3.91
4073 4542 4.101448 GGCTGGATGGACCGTGCT 62.101 66.667 6.77 0.00 42.61 4.40
4085 4554 2.813908 GCCTACGTGTTCGGCTGG 60.814 66.667 0.00 0.00 40.62 4.85
4090 4559 1.226491 CCTACCGCCTACGTGTTCG 60.226 63.158 0.00 0.00 43.34 3.95
4091 4560 1.517913 GCCTACCGCCTACGTGTTC 60.518 63.158 0.00 0.00 37.70 3.18
4131 4602 3.128375 CCCACACACAACAAGGCC 58.872 61.111 0.00 0.00 0.00 5.19
4144 4615 1.227853 ACTTGTCAGTTCGGCCCAC 60.228 57.895 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.