Multiple sequence alignment - TraesCS1B01G027800

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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 TraesCS1B01G027800 chr1B 100.000 2622 0 0 1 2622 13449495 13446874 0.000000e+00 4843.0
1 TraesCS1B01G027800 chr1B 89.648 1903 128 31 747 2622 12976353 12974493 0.000000e+00 2359.0
2 TraesCS1B01G027800 chr1B 88.599 1342 103 24 743 2067 12388442 12387134 0.000000e+00 1585.0
3 TraesCS1B01G027800 chr1B 88.143 1341 114 25 743 2067 12738960 12737649 0.000000e+00 1554.0
4 TraesCS1B01G027800 chr1B 80.721 1276 157 51 811 2067 12754835 12753630 0.000000e+00 911.0
5 TraesCS1B01G027800 chr1B 84.912 285 34 6 1375 1653 13046567 13046848 1.990000e-71 279.0
6 TraesCS1B01G027800 chr1B 86.893 206 20 4 545 743 12976610 12976405 9.440000e-55 224.0
7 TraesCS1B01G027800 chr1B 85.204 196 27 2 549 742 12746617 12746422 1.590000e-47 200.0
8 TraesCS1B01G027800 chr1B 94.792 96 5 0 746 841 12401864 12401769 1.630000e-32 150.0
9 TraesCS1B01G027800 chr1B 95.745 47 2 0 661 707 12976571 12976525 2.800000e-10 76.8
10 TraesCS1B01G027800 chr1A 86.598 1552 135 40 545 2067 10607960 10606453 0.000000e+00 1646.0
11 TraesCS1B01G027800 chr1A 92.421 541 36 4 1 540 347419228 347418692 0.000000e+00 767.0
12 TraesCS1B01G027800 chr1D 89.466 1291 114 14 743 2025 9364879 9363603 0.000000e+00 1611.0
13 TraesCS1B01G027800 chr1D 84.957 811 103 16 1266 2067 9367445 9366645 0.000000e+00 804.0
14 TraesCS1B01G027800 chr1D 93.346 541 31 4 1 540 487307504 487306968 0.000000e+00 795.0
15 TraesCS1B01G027800 chr1D 81.349 1008 130 31 1071 2067 9395592 9394632 0.000000e+00 767.0
16 TraesCS1B01G027800 chr1D 92.421 541 35 5 1 540 30698435 30697900 0.000000e+00 767.0
17 TraesCS1B01G027800 chr1D 80.381 1101 125 50 778 1837 9400583 9399533 0.000000e+00 752.0
18 TraesCS1B01G027800 chr1D 80.682 176 20 7 772 935 9397946 9397773 9.850000e-25 124.0
19 TraesCS1B01G027800 chr1D 91.566 83 7 0 661 743 9365015 9364933 5.930000e-22 115.0
20 TraesCS1B01G027800 chr3D 94.085 541 27 4 1 540 516403794 516403258 0.000000e+00 817.0
21 TraesCS1B01G027800 chr3D 93.530 541 30 4 1 540 465175561 465176097 0.000000e+00 800.0
22 TraesCS1B01G027800 chr2B 93.173 542 31 5 1 540 431226 431763 0.000000e+00 791.0
23 TraesCS1B01G027800 chr2B 85.227 352 38 10 2071 2419 139806296 139806636 1.490000e-92 350.0
24 TraesCS1B01G027800 chr2B 82.482 274 42 4 2070 2343 556598351 556598618 4.360000e-58 235.0
25 TraesCS1B01G027800 chr6A 92.791 541 34 4 1 540 276498937 276499473 0.000000e+00 778.0
26 TraesCS1B01G027800 chr4B 92.791 541 32 6 1 540 272432977 272432443 0.000000e+00 776.0
27 TraesCS1B01G027800 chr4B 84.091 352 37 15 2070 2419 235376067 235376401 3.260000e-84 322.0
28 TraesCS1B01G027800 chr7A 92.322 547 35 6 1 546 158659825 158660365 0.000000e+00 771.0
29 TraesCS1B01G027800 chr4A 82.390 318 46 5 2070 2384 668107501 668107191 4.300000e-68 268.0
30 TraesCS1B01G027800 chr4A 80.435 368 44 17 2068 2419 39527984 39527629 3.350000e-64 255.0
31 TraesCS1B01G027800 chr7D 81.525 341 43 9 2071 2409 53482400 53482078 2.000000e-66 263.0
32 TraesCS1B01G027800 chr5D 80.618 356 45 19 2071 2414 442891580 442891923 1.200000e-63 254.0
33 TraesCS1B01G027800 chr5D 86.391 169 16 6 2071 2239 354506936 354507097 7.460000e-41 178.0
34 TraesCS1B01G027800 chr2D 79.943 349 54 12 2071 2418 97226500 97226833 2.610000e-60 243.0
35 TraesCS1B01G027800 chr5A 80.352 341 48 10 2070 2406 697621198 697621523 9.380000e-60 241.0
36 TraesCS1B01G027800 chrUn 88.372 129 10 4 2291 2419 134451839 134451962 1.630000e-32 150.0
37 TraesCS1B01G027800 chrUn 87.597 129 12 4 2291 2419 30576467 30576591 2.100000e-31 147.0
38 TraesCS1B01G027800 chr6D 89.431 123 8 4 2297 2419 1012652 1012535 1.630000e-32 150.0


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 TraesCS1B01G027800 chr1B 13446874 13449495 2621 True 4843.000000 4843 100.000 1 2622 1 chr1B.!!$R6 2621
1 TraesCS1B01G027800 chr1B 12387134 12388442 1308 True 1585.000000 1585 88.599 743 2067 1 chr1B.!!$R1 1324
2 TraesCS1B01G027800 chr1B 12737649 12738960 1311 True 1554.000000 1554 88.143 743 2067 1 chr1B.!!$R3 1324
3 TraesCS1B01G027800 chr1B 12753630 12754835 1205 True 911.000000 911 80.721 811 2067 1 chr1B.!!$R5 1256
4 TraesCS1B01G027800 chr1B 12974493 12976610 2117 True 886.600000 2359 90.762 545 2622 3 chr1B.!!$R7 2077
5 TraesCS1B01G027800 chr1A 10606453 10607960 1507 True 1646.000000 1646 86.598 545 2067 1 chr1A.!!$R1 1522
6 TraesCS1B01G027800 chr1A 347418692 347419228 536 True 767.000000 767 92.421 1 540 1 chr1A.!!$R2 539
7 TraesCS1B01G027800 chr1D 9363603 9367445 3842 True 843.333333 1611 88.663 661 2067 3 chr1D.!!$R3 1406
8 TraesCS1B01G027800 chr1D 487306968 487307504 536 True 795.000000 795 93.346 1 540 1 chr1D.!!$R2 539
9 TraesCS1B01G027800 chr1D 30697900 30698435 535 True 767.000000 767 92.421 1 540 1 chr1D.!!$R1 539
10 TraesCS1B01G027800 chr1D 9394632 9400583 5951 True 547.666667 767 80.804 772 2067 3 chr1D.!!$R4 1295
11 TraesCS1B01G027800 chr3D 516403258 516403794 536 True 817.000000 817 94.085 1 540 1 chr3D.!!$R1 539
12 TraesCS1B01G027800 chr3D 465175561 465176097 536 False 800.000000 800 93.530 1 540 1 chr3D.!!$F1 539
13 TraesCS1B01G027800 chr2B 431226 431763 537 False 791.000000 791 93.173 1 540 1 chr2B.!!$F1 539
14 TraesCS1B01G027800 chr6A 276498937 276499473 536 False 778.000000 778 92.791 1 540 1 chr6A.!!$F1 539
15 TraesCS1B01G027800 chr4B 272432443 272432977 534 True 776.000000 776 92.791 1 540 1 chr4B.!!$R1 539
16 TraesCS1B01G027800 chr7A 158659825 158660365 540 False 771.000000 771 92.322 1 546 1 chr7A.!!$F1 545

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
68 69 0.173481 GGATCTGTACGCTGCTGACA 59.827 55.0 0.00 0.57 0.00 3.58 F
606 609 0.453390 GCTGCAGCCACCAACTAATC 59.547 55.0 28.76 0.00 34.31 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1264 3295 0.173029 CCACAGTTGTTGCAGCACAA 59.827 50.0 1.37 0.43 34.15 3.33 R
2506 9272 0.247185 TGCATGCACTCGACAGATCA 59.753 50.0 18.46 0.00 0.00 2.92 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 1.507140 TATCGGTTGGAGGCTTGGAT 58.493 50.000 0.00 0.00 0.00 3.41
56 57 0.329596 GGTTGGAGGCTTGGATCTGT 59.670 55.000 0.00 0.00 0.00 3.41
61 62 0.461961 GAGGCTTGGATCTGTACGCT 59.538 55.000 0.00 0.00 0.00 5.07
68 69 0.173481 GGATCTGTACGCTGCTGACA 59.827 55.000 0.00 0.57 0.00 3.58
94 95 2.986290 CCACCATGCCAGACGGTA 59.014 61.111 0.00 0.00 33.28 4.02
95 96 1.449601 CCACCATGCCAGACGGTAC 60.450 63.158 0.00 0.00 33.28 3.34
138 139 4.162320 CACTGGACCTTAATCCTCTTGCTA 59.838 45.833 0.00 0.00 39.75 3.49
221 222 3.055144 GCCTTGCTAATTGCTTGGC 57.945 52.632 14.77 14.77 46.41 4.52
245 246 9.595823 GGCTAGTTTACTACAGAAATTGTATGA 57.404 33.333 0.00 0.00 41.30 2.15
288 291 3.422796 AGAAGTAACTGAGAAGCGAGGA 58.577 45.455 0.00 0.00 0.00 3.71
308 311 8.173775 GCGAGGAGTGATGATAATTTATTCATG 58.826 37.037 3.72 0.00 0.00 3.07
584 587 1.522258 CAATAAAATCAATGCGGCGGC 59.478 47.619 9.78 9.68 40.52 6.53
601 604 4.332637 CACGCTGCAGCCACCAAC 62.333 66.667 32.07 4.04 37.91 3.77
603 606 2.358615 CGCTGCAGCCACCAACTA 60.359 61.111 32.07 0.00 37.91 2.24
604 607 1.965930 CGCTGCAGCCACCAACTAA 60.966 57.895 32.07 0.00 37.91 2.24
605 608 1.308069 CGCTGCAGCCACCAACTAAT 61.308 55.000 32.07 0.00 37.91 1.73
606 609 0.453390 GCTGCAGCCACCAACTAATC 59.547 55.000 28.76 0.00 34.31 1.75
607 610 1.098050 CTGCAGCCACCAACTAATCC 58.902 55.000 0.00 0.00 0.00 3.01
609 612 1.005805 TGCAGCCACCAACTAATCCAT 59.994 47.619 0.00 0.00 0.00 3.41
611 614 3.117550 TGCAGCCACCAACTAATCCATAT 60.118 43.478 0.00 0.00 0.00 1.78
612 615 3.254166 GCAGCCACCAACTAATCCATATG 59.746 47.826 0.00 0.00 0.00 1.78
613 616 4.464008 CAGCCACCAACTAATCCATATGT 58.536 43.478 1.24 0.00 0.00 2.29
614 617 4.276678 CAGCCACCAACTAATCCATATGTG 59.723 45.833 1.24 0.00 0.00 3.21
617 620 5.359576 GCCACCAACTAATCCATATGTGAAA 59.640 40.000 1.24 0.00 0.00 2.69
618 621 6.127479 GCCACCAACTAATCCATATGTGAAAA 60.127 38.462 1.24 0.00 0.00 2.29
619 622 7.483307 CCACCAACTAATCCATATGTGAAAAG 58.517 38.462 1.24 3.99 0.00 2.27
620 623 6.974622 CACCAACTAATCCATATGTGAAAAGC 59.025 38.462 1.24 0.00 0.00 3.51
621 624 6.096846 ACCAACTAATCCATATGTGAAAAGCC 59.903 38.462 1.24 0.00 0.00 4.35
622 625 6.096705 CCAACTAATCCATATGTGAAAAGCCA 59.903 38.462 1.24 0.00 0.00 4.75
624 627 7.338800 ACTAATCCATATGTGAAAAGCCAAG 57.661 36.000 1.24 0.00 0.00 3.61
625 628 5.603170 AATCCATATGTGAAAAGCCAAGG 57.397 39.130 1.24 0.00 0.00 3.61
626 629 2.760092 TCCATATGTGAAAAGCCAAGGC 59.240 45.455 2.02 2.02 42.33 4.35
643 646 2.186903 CGGAGCGTGCCTTACCAT 59.813 61.111 0.00 0.00 0.00 3.55
644 647 1.883084 CGGAGCGTGCCTTACCATC 60.883 63.158 0.00 0.00 0.00 3.51
645 648 1.522569 GGAGCGTGCCTTACCATCT 59.477 57.895 0.00 0.00 0.00 2.90
647 650 1.269831 GGAGCGTGCCTTACCATCTAG 60.270 57.143 0.00 0.00 0.00 2.43
648 651 1.409427 GAGCGTGCCTTACCATCTAGT 59.591 52.381 0.00 0.00 0.00 2.57
650 653 3.028850 AGCGTGCCTTACCATCTAGTAA 58.971 45.455 0.00 0.00 0.00 2.24
652 655 4.081309 AGCGTGCCTTACCATCTAGTAAAA 60.081 41.667 0.00 0.00 32.02 1.52
654 657 5.050295 GCGTGCCTTACCATCTAGTAAAATC 60.050 44.000 0.00 0.00 32.02 2.17
657 660 7.465513 CGTGCCTTACCATCTAGTAAAATCAAC 60.466 40.741 0.00 0.00 32.02 3.18
658 661 7.335924 GTGCCTTACCATCTAGTAAAATCAACA 59.664 37.037 0.00 0.00 32.02 3.33
659 662 7.335924 TGCCTTACCATCTAGTAAAATCAACAC 59.664 37.037 0.00 0.00 32.02 3.32
660 663 7.465513 GCCTTACCATCTAGTAAAATCAACACG 60.466 40.741 0.00 0.00 32.02 4.49
720 2649 1.991121 AGGTGGTACTTGACTCGACA 58.009 50.000 0.00 0.00 0.00 4.35
729 2658 1.524355 CTTGACTCGACACACTGCAAG 59.476 52.381 0.00 0.00 42.29 4.01
749 2732 1.526686 TCTGCAGCCACCAGTTGTG 60.527 57.895 9.47 0.00 45.01 3.33
799 2782 1.803453 AACACATGGAGGCCACCCAT 61.803 55.000 20.32 20.32 44.75 4.00
870 2872 2.827642 GCCCACATGCTCTCTGCC 60.828 66.667 0.00 0.00 42.00 4.85
1043 3063 8.258007 CAGTCCCTGTTACATATTCAGTCTTTA 58.742 37.037 0.00 0.00 0.00 1.85
1046 3066 8.258007 TCCCTGTTACATATTCAGTCTTTACAG 58.742 37.037 0.00 0.00 0.00 2.74
1158 3178 2.113774 CCACAGCCAAGGTGAGCA 59.886 61.111 0.05 0.00 38.54 4.26
1195 3221 6.678568 TCTTTGTCTTTCTTCATCTCCTCT 57.321 37.500 0.00 0.00 0.00 3.69
1213 3239 4.080469 TCCTCTCCGAGTAAGTCAGTGTAT 60.080 45.833 0.00 0.00 0.00 2.29
1257 3288 4.643387 GCAGGTGCGACCCCAAGT 62.643 66.667 2.18 0.00 39.75 3.16
1264 3295 4.657824 CGACCCCAAGTGCGTCGT 62.658 66.667 9.66 0.00 43.29 4.34
1450 3481 3.136791 GCAGCTGCACTAAGGCCC 61.137 66.667 33.36 0.00 41.59 5.80
1483 3515 1.014352 GTTGTCGCCCGAATAATGCT 58.986 50.000 0.00 0.00 0.00 3.79
1569 3611 6.474630 AGATGCAGAGAAGAAATGAGAGTTT 58.525 36.000 0.00 0.00 0.00 2.66
1571 3613 7.765360 AGATGCAGAGAAGAAATGAGAGTTTAG 59.235 37.037 0.00 0.00 0.00 1.85
1582 3624 1.325943 GAGAGTTTAGTGCATGCTCGC 59.674 52.381 20.33 9.20 0.00 5.03
1659 8390 7.763172 TTATTAAACCATTTATGCTTTGCGG 57.237 32.000 0.00 0.00 0.00 5.69
1669 8400 0.814457 TGCTTTGCGGCCGATAAAAT 59.186 45.000 33.48 0.00 0.00 1.82
1678 8409 2.518949 GGCCGATAAAATGCATATGCG 58.481 47.619 22.21 6.18 45.83 4.73
1728 8462 9.811995 CAAATCAAAATCATCTACCATGAATGT 57.188 29.630 0.00 0.00 0.00 2.71
1953 8697 5.040635 ACCAAAAATGTCAACATCGTGTTC 58.959 37.500 0.00 0.00 38.77 3.18
2119 8867 4.467082 ACATTCTCCTGCATGCCAAAAATA 59.533 37.500 16.68 0.00 0.00 1.40
2125 8873 6.052405 TCCTGCATGCCAAAAATAGATTTT 57.948 33.333 16.68 0.00 41.93 1.82
2226 8974 6.152379 GGAAAGACTTAAGCATTTTGACCTG 58.848 40.000 1.29 0.00 0.00 4.00
2230 8978 3.636300 ACTTAAGCATTTTGACCTGTGCA 59.364 39.130 1.29 0.00 39.94 4.57
2254 9002 3.519774 AAAAACAAGTCGAACGCCG 57.480 47.368 0.00 0.00 40.25 6.46
2255 9003 0.028374 AAAAACAAGTCGAACGCCGG 59.972 50.000 0.00 0.00 39.14 6.13
2305 9053 5.425217 TCACTAATGAAGAACTGCTATCCCA 59.575 40.000 0.00 0.00 0.00 4.37
2315 9063 2.025605 ACTGCTATCCCATATGGCATGG 60.026 50.000 16.97 10.59 35.04 3.66
2325 9073 5.427806 TCCCATATGGCATGGAAATTTTCAA 59.572 36.000 16.97 0.00 41.64 2.69
2327 9075 5.237779 CCATATGGCATGGAAATTTTCAAGC 59.762 40.000 16.67 16.67 41.64 4.01
2328 9076 3.766068 TGGCATGGAAATTTTCAAGCA 57.234 38.095 24.03 10.67 0.00 3.91
2439 9205 4.934515 GGAACCAAAATTCCGTGTACAAA 58.065 39.130 0.00 0.00 38.95 2.83
2469 9235 5.529581 AAATTTAAACCCGCTATGGATGG 57.470 39.130 0.00 0.00 42.00 3.51
2491 9257 9.727627 GATGGTTGAGATCAATTTGAGTATTTC 57.272 33.333 5.21 0.00 38.24 2.17
2506 9272 9.739276 TTTGAGTATTTCATCTCATGTTTAGGT 57.261 29.630 0.00 0.00 39.85 3.08
2507 9273 8.722480 TGAGTATTTCATCTCATGTTTAGGTG 57.278 34.615 0.00 0.00 36.04 4.00
2513 9279 6.550938 TCATCTCATGTTTAGGTGATCTGT 57.449 37.500 0.00 0.00 29.11 3.41
2515 9281 4.998788 TCTCATGTTTAGGTGATCTGTCG 58.001 43.478 0.00 0.00 0.00 4.35
2516 9282 4.705023 TCTCATGTTTAGGTGATCTGTCGA 59.295 41.667 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.290386 GGATACACAAGTCGATAAAGAGGG 58.710 45.833 0.00 0.00 0.00 4.30
52 53 1.289066 GGTGTCAGCAGCGTACAGA 59.711 57.895 3.34 0.00 33.19 3.41
94 95 1.300931 CACTAGTGCTGGTGCGTGT 60.301 57.895 10.54 0.00 43.34 4.49
95 96 3.554232 CACTAGTGCTGGTGCGTG 58.446 61.111 10.54 0.00 43.34 5.34
138 139 1.898574 CAACAAGGAGCCGCAACCT 60.899 57.895 3.71 3.71 38.23 3.50
308 311 1.137086 ACCGATGCAGTGGACATCTAC 59.863 52.381 13.56 0.00 41.45 2.59
414 417 9.574516 GATAATTTGTAGGGACCTGACAATTAT 57.425 33.333 15.84 15.84 33.33 1.28
417 420 6.055588 CGATAATTTGTAGGGACCTGACAAT 58.944 40.000 11.12 2.85 33.33 2.71
418 421 5.424757 CGATAATTTGTAGGGACCTGACAA 58.575 41.667 0.00 7.43 0.00 3.18
419 422 4.682320 GCGATAATTTGTAGGGACCTGACA 60.682 45.833 0.00 0.00 0.00 3.58
420 423 3.808174 GCGATAATTTGTAGGGACCTGAC 59.192 47.826 0.00 0.00 0.00 3.51
421 424 3.709653 AGCGATAATTTGTAGGGACCTGA 59.290 43.478 0.00 0.00 0.00 3.86
422 425 4.073293 AGCGATAATTTGTAGGGACCTG 57.927 45.455 0.00 0.00 0.00 4.00
425 428 5.813672 TGTGTAAGCGATAATTTGTAGGGAC 59.186 40.000 0.00 0.00 0.00 4.46
584 587 4.332637 GTTGGTGGCTGCAGCGTG 62.333 66.667 31.19 0.00 43.26 5.34
586 589 1.308069 ATTAGTTGGTGGCTGCAGCG 61.308 55.000 31.19 0.00 43.26 5.18
587 590 0.453390 GATTAGTTGGTGGCTGCAGC 59.547 55.000 30.88 30.88 41.14 5.25
588 591 1.098050 GGATTAGTTGGTGGCTGCAG 58.902 55.000 10.11 10.11 0.00 4.41
589 592 0.403655 TGGATTAGTTGGTGGCTGCA 59.596 50.000 0.50 0.00 0.00 4.41
590 593 1.767759 ATGGATTAGTTGGTGGCTGC 58.232 50.000 0.00 0.00 0.00 5.25
591 594 4.276678 CACATATGGATTAGTTGGTGGCTG 59.723 45.833 7.80 0.00 0.00 4.85
592 595 4.165950 TCACATATGGATTAGTTGGTGGCT 59.834 41.667 7.80 0.00 0.00 4.75
593 596 4.460263 TCACATATGGATTAGTTGGTGGC 58.540 43.478 7.80 0.00 0.00 5.01
594 597 7.403312 TTTTCACATATGGATTAGTTGGTGG 57.597 36.000 7.80 0.00 0.00 4.61
595 598 6.974622 GCTTTTCACATATGGATTAGTTGGTG 59.025 38.462 7.80 0.00 0.00 4.17
596 599 6.096846 GGCTTTTCACATATGGATTAGTTGGT 59.903 38.462 7.80 0.00 0.00 3.67
600 603 6.322201 CCTTGGCTTTTCACATATGGATTAGT 59.678 38.462 7.80 0.00 0.00 2.24
601 604 6.736794 GCCTTGGCTTTTCACATATGGATTAG 60.737 42.308 7.80 3.92 0.00 1.73
603 606 4.141869 GCCTTGGCTTTTCACATATGGATT 60.142 41.667 7.80 0.00 0.00 3.01
604 607 3.385755 GCCTTGGCTTTTCACATATGGAT 59.614 43.478 7.80 0.00 0.00 3.41
605 608 2.760092 GCCTTGGCTTTTCACATATGGA 59.240 45.455 7.80 0.00 0.00 3.41
606 609 2.480073 CGCCTTGGCTTTTCACATATGG 60.480 50.000 7.80 0.00 0.00 2.74
607 610 2.480073 CCGCCTTGGCTTTTCACATATG 60.480 50.000 10.12 0.00 0.00 1.78
609 612 1.173043 CCGCCTTGGCTTTTCACATA 58.827 50.000 10.12 0.00 0.00 2.29
611 614 1.152860 TCCGCCTTGGCTTTTCACA 60.153 52.632 10.12 0.00 37.80 3.58
612 615 1.581447 CTCCGCCTTGGCTTTTCAC 59.419 57.895 10.12 0.00 37.80 3.18
613 616 2.268076 GCTCCGCCTTGGCTTTTCA 61.268 57.895 10.12 0.00 37.80 2.69
614 617 2.568612 GCTCCGCCTTGGCTTTTC 59.431 61.111 10.12 0.00 37.80 2.29
625 628 4.752879 TGGTAAGGCACGCTCCGC 62.753 66.667 0.00 0.00 0.00 5.54
626 629 1.883084 GATGGTAAGGCACGCTCCG 60.883 63.158 0.00 0.00 0.00 4.63
627 630 0.750850 TAGATGGTAAGGCACGCTCC 59.249 55.000 0.00 0.00 0.00 4.70
628 631 1.409427 ACTAGATGGTAAGGCACGCTC 59.591 52.381 0.00 0.00 0.00 5.03
629 632 1.486211 ACTAGATGGTAAGGCACGCT 58.514 50.000 0.00 0.00 0.00 5.07
630 633 3.447918 TTACTAGATGGTAAGGCACGC 57.552 47.619 0.00 0.00 0.00 5.34
631 634 6.046593 TGATTTTACTAGATGGTAAGGCACG 58.953 40.000 0.00 0.00 33.90 5.34
632 635 7.335924 TGTTGATTTTACTAGATGGTAAGGCAC 59.664 37.037 0.00 0.00 33.90 5.01
633 636 7.335924 GTGTTGATTTTACTAGATGGTAAGGCA 59.664 37.037 0.00 0.00 33.90 4.75
634 637 7.465513 CGTGTTGATTTTACTAGATGGTAAGGC 60.466 40.741 0.00 0.00 33.90 4.35
635 638 7.465513 GCGTGTTGATTTTACTAGATGGTAAGG 60.466 40.741 0.00 0.00 33.90 2.69
636 639 7.064134 TGCGTGTTGATTTTACTAGATGGTAAG 59.936 37.037 0.00 0.00 33.90 2.34
638 641 6.311935 GTGCGTGTTGATTTTACTAGATGGTA 59.688 38.462 0.00 0.00 0.00 3.25
639 642 5.121768 GTGCGTGTTGATTTTACTAGATGGT 59.878 40.000 0.00 0.00 0.00 3.55
640 643 5.560148 GTGCGTGTTGATTTTACTAGATGG 58.440 41.667 0.00 0.00 0.00 3.51
643 646 3.122278 GCGTGCGTGTTGATTTTACTAGA 59.878 43.478 0.00 0.00 0.00 2.43
644 647 3.120820 TGCGTGCGTGTTGATTTTACTAG 60.121 43.478 0.00 0.00 0.00 2.57
645 648 2.801111 TGCGTGCGTGTTGATTTTACTA 59.199 40.909 0.00 0.00 0.00 1.82
647 650 1.969256 CTGCGTGCGTGTTGATTTTAC 59.031 47.619 0.00 0.00 0.00 2.01
648 651 1.661743 GCTGCGTGCGTGTTGATTTTA 60.662 47.619 0.00 0.00 0.00 1.52
650 653 1.370414 GCTGCGTGCGTGTTGATTT 60.370 52.632 0.00 0.00 0.00 2.17
652 655 2.448153 CTTGCTGCGTGCGTGTTGAT 62.448 55.000 0.00 0.00 46.63 2.57
654 657 2.723271 CTTGCTGCGTGCGTGTTG 60.723 61.111 0.00 0.00 46.63 3.33
660 663 3.771568 TTTGTGGCTTGCTGCGTGC 62.772 57.895 7.93 7.93 44.05 5.34
676 2447 4.202212 GGCTTTTCACACATGGGTTAGTTT 60.202 41.667 0.00 0.00 0.00 2.66
729 2658 2.113986 AACTGGTGGCTGCAGACC 59.886 61.111 19.23 17.32 0.00 3.85
749 2732 7.333672 ACGTAAATCTATTCAGAAAGGTTGACC 59.666 37.037 0.00 0.00 33.50 4.02
755 2738 7.827819 TCACACGTAAATCTATTCAGAAAGG 57.172 36.000 0.00 0.00 33.50 3.11
788 2771 1.067295 TCATATCCATGGGTGGCCTC 58.933 55.000 13.02 0.00 45.63 4.70
799 2782 3.612517 GCACGAGGCATCATATCCA 57.387 52.632 0.00 0.00 43.97 3.41
960 2976 1.239347 GGAATGCCGGGCTTCTTATC 58.761 55.000 21.46 8.08 0.00 1.75
1195 3221 2.941064 CGGATACACTGACTTACTCGGA 59.059 50.000 0.00 0.00 0.00 4.55
1213 3239 1.403647 CGACCAATGTCAGTAAGCGGA 60.404 52.381 0.00 0.00 41.85 5.54
1257 3288 3.198489 TTGCAGCACAACGACGCA 61.198 55.556 0.00 0.00 31.73 5.24
1264 3295 0.173029 CCACAGTTGTTGCAGCACAA 59.827 50.000 1.37 0.43 34.15 3.33
1460 3491 1.717194 TTATTCGGGCGACAACAGAC 58.283 50.000 0.00 0.00 0.00 3.51
1461 3492 2.276201 CATTATTCGGGCGACAACAGA 58.724 47.619 0.00 0.00 0.00 3.41
1536 3574 4.540715 TCTTCTCTGCATCTACCAGATCA 58.459 43.478 0.00 0.00 38.54 2.92
1569 3611 0.740868 GGAACAGCGAGCATGCACTA 60.741 55.000 21.98 0.00 37.31 2.74
1571 3613 1.580845 AAGGAACAGCGAGCATGCAC 61.581 55.000 21.98 13.43 37.31 4.57
1582 3624 7.496529 TTATTTCAGACACAAGAAGGAACAG 57.503 36.000 0.00 0.00 0.00 3.16
1659 8390 2.910482 CACGCATATGCATTTTATCGGC 59.090 45.455 26.52 0.00 42.21 5.54
1669 8400 2.049888 TTCCATTCCACGCATATGCA 57.950 45.000 26.52 7.82 42.21 3.96
1678 8409 7.954835 TGAATTCATATTCCATTCCATTCCAC 58.045 34.615 3.38 0.00 39.56 4.02
1708 8439 7.348815 TCCTGACATTCATGGTAGATGATTTT 58.651 34.615 0.00 0.00 0.00 1.82
1724 8458 4.712829 TCAATGCATTCCATTCCTGACATT 59.287 37.500 9.53 0.00 42.15 2.71
1726 8460 3.699413 TCAATGCATTCCATTCCTGACA 58.301 40.909 9.53 0.00 42.15 3.58
1727 8461 4.556104 CGATCAATGCATTCCATTCCTGAC 60.556 45.833 9.53 0.00 42.15 3.51
1728 8462 3.566742 CGATCAATGCATTCCATTCCTGA 59.433 43.478 9.53 2.12 42.15 3.86
1754 8489 4.059511 GCTCTCCATCTTGATGATCTGTG 58.940 47.826 11.76 0.00 32.05 3.66
1758 8493 4.202233 TGACAGCTCTCCATCTTGATGATC 60.202 45.833 11.76 0.00 32.05 2.92
1986 8730 8.522830 CCTAAACAAGCTAAATCATCTCCAAAA 58.477 33.333 0.00 0.00 0.00 2.44
2027 8774 3.941483 GTGCATATAGACTTGCCAACTGT 59.059 43.478 0.00 0.00 38.08 3.55
2100 8848 3.966979 TCTATTTTTGGCATGCAGGAGA 58.033 40.909 21.36 8.60 0.00 3.71
2145 8893 7.132213 CGACAATGAACACATCTAGTTTTGTT 58.868 34.615 5.26 5.26 32.87 2.83
2195 8943 9.487790 CAAAATGCTTAAGTCTTTCCCATAAAA 57.512 29.630 4.02 0.00 0.00 1.52
2200 8948 5.010617 GGTCAAAATGCTTAAGTCTTTCCCA 59.989 40.000 4.02 0.00 0.00 4.37
2207 8955 4.229876 GCACAGGTCAAAATGCTTAAGTC 58.770 43.478 4.02 0.00 35.16 3.01
2208 8956 3.636300 TGCACAGGTCAAAATGCTTAAGT 59.364 39.130 4.02 0.00 38.90 2.24
2209 8957 4.241590 TGCACAGGTCAAAATGCTTAAG 57.758 40.909 0.00 0.00 38.90 1.85
2210 8958 4.662468 TTGCACAGGTCAAAATGCTTAA 57.338 36.364 0.00 0.00 38.90 1.85
2211 8959 4.662468 TTTGCACAGGTCAAAATGCTTA 57.338 36.364 0.00 0.00 38.90 3.09
2212 8960 3.540314 TTTGCACAGGTCAAAATGCTT 57.460 38.095 0.00 0.00 38.90 3.91
2213 8961 3.540314 TTTTGCACAGGTCAAAATGCT 57.460 38.095 0.00 0.00 38.17 3.79
2244 8992 0.733566 TGTAACATCCGGCGTTCGAC 60.734 55.000 11.79 7.28 42.43 4.20
2250 8998 4.609691 AAATTAAGTGTAACATCCGGCG 57.390 40.909 0.00 0.00 41.43 6.46
2279 9027 6.823689 GGGATAGCAGTTCTTCATTAGTGAAA 59.176 38.462 2.06 0.00 43.39 2.69
2281 9029 5.425217 TGGGATAGCAGTTCTTCATTAGTGA 59.575 40.000 0.00 0.00 0.00 3.41
2282 9030 5.674525 TGGGATAGCAGTTCTTCATTAGTG 58.325 41.667 0.00 0.00 0.00 2.74
2283 9031 5.957771 TGGGATAGCAGTTCTTCATTAGT 57.042 39.130 0.00 0.00 0.00 2.24
2285 9033 7.397221 CCATATGGGATAGCAGTTCTTCATTA 58.603 38.462 14.52 0.00 40.01 1.90
2286 9034 6.243900 CCATATGGGATAGCAGTTCTTCATT 58.756 40.000 14.52 0.00 40.01 2.57
2293 9041 3.562826 CCATGCCATATGGGATAGCAGTT 60.563 47.826 26.44 2.87 44.94 3.16
2305 9053 5.818857 GTGCTTGAAAATTTCCATGCCATAT 59.181 36.000 11.84 0.00 33.97 1.78
2327 9075 5.631929 TGTTCGTATTAGTGTAGCAAGTGTG 59.368 40.000 0.00 0.00 0.00 3.82
2328 9076 5.775686 TGTTCGTATTAGTGTAGCAAGTGT 58.224 37.500 0.00 0.00 0.00 3.55
2409 9158 6.092748 CACGGAATTTTGGTTCCTAATGAAG 58.907 40.000 4.37 0.00 44.43 3.02
2443 9209 7.201875 CCATCCATAGCGGGTTTAAATTTAGTT 60.202 37.037 0.00 0.00 34.36 2.24
2459 9225 6.263842 TCAAATTGATCTCAACCATCCATAGC 59.736 38.462 0.00 0.00 38.86 2.97
2462 9228 6.192773 ACTCAAATTGATCTCAACCATCCAT 58.807 36.000 0.00 0.00 38.86 3.41
2491 9257 5.461407 CGACAGATCACCTAAACATGAGATG 59.539 44.000 0.00 0.00 0.00 2.90
2506 9272 0.247185 TGCATGCACTCGACAGATCA 59.753 50.000 18.46 0.00 0.00 2.92
2507 9273 0.649475 GTGCATGCACTCGACAGATC 59.351 55.000 37.48 12.32 43.12 2.75


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

AutoCloner maintained by Alex Coulton.