Multiple sequence alignment - TraesCS6B01G049400

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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 TraesCS6B01G049400 chr6B 100.000 2535 0 0 1 2535 29061592 29059058 0.000000e+00 4682.0
1 TraesCS6B01G049400 chr6B 89.940 1342 90 26 451 1769 28980779 28979460 0.000000e+00 1688.0
2 TraesCS6B01G049400 chr6B 88.657 767 49 17 807 1550 28925846 28926597 0.000000e+00 900.0
3 TraesCS6B01G049400 chr6B 88.026 760 55 20 807 1550 28256813 28256074 0.000000e+00 867.0
4 TraesCS6B01G049400 chr6B 85.440 364 52 1 1 364 28981149 28980787 6.620000e-101 377.0
5 TraesCS6B01G049400 chr6B 93.717 191 11 1 2234 2423 28978591 28978401 4.130000e-73 285.0
6 TraesCS6B01G049400 chr6B 95.349 43 2 0 2493 2535 28977983 28977941 4.530000e-08 69.4
7 TraesCS6B01G049400 chr6D 85.570 2176 169 57 1 2096 16524172 16522062 0.000000e+00 2145.0
8 TraesCS6B01G049400 chr6D 89.330 806 70 9 736 1535 16502655 16503450 0.000000e+00 998.0
9 TraesCS6B01G049400 chr6D 91.469 211 13 4 2216 2423 16522010 16521802 4.130000e-73 285.0
10 TraesCS6B01G049400 chr6A 87.908 1778 157 30 1 1753 16721180 16719436 0.000000e+00 2039.0
11 TraesCS6B01G049400 chr6A 88.701 770 54 21 800 1550 16593984 16593229 0.000000e+00 909.0
12 TraesCS6B01G049400 chr6A 87.990 766 59 23 807 1550 16658878 16658124 0.000000e+00 874.0
13 TraesCS6B01G049400 chr1B 87.411 1263 81 38 538 1770 587472429 587473643 0.000000e+00 1380.0
14 TraesCS6B01G049400 chr1B 92.647 204 11 3 2218 2418 587474103 587474305 8.870000e-75 291.0
15 TraesCS6B01G049400 chr1B 86.282 277 10 6 1883 2151 587473820 587474076 2.480000e-70 276.0
16 TraesCS6B01G049400 chr1B 86.957 92 3 3 2453 2535 587474490 587474581 7.470000e-16 95.3
17 TraesCS6B01G049400 chr2D 97.917 48 1 0 2177 2224 517308068 517308115 1.620000e-12 84.2
18 TraesCS6B01G049400 chr3B 94.340 53 2 1 2170 2221 825250060 825250112 2.090000e-11 80.5
19 TraesCS6B01G049400 chr3B 94.231 52 2 1 2170 2221 774226148 774226198 7.520000e-11 78.7
20 TraesCS6B01G049400 chr7B 95.918 49 1 1 2174 2221 217970609 217970657 7.520000e-11 78.7
21 TraesCS6B01G049400 chr7B 90.164 61 3 3 2158 2217 261986882 261986824 2.700000e-10 76.8
22 TraesCS6B01G049400 chr4B 91.379 58 3 2 2177 2232 391554368 391554425 7.520000e-11 78.7
23 TraesCS6B01G049400 chr2B 92.593 54 4 0 2172 2225 695378401 695378454 7.520000e-11 78.7
24 TraesCS6B01G049400 chr2A 91.228 57 5 0 2170 2226 549890419 549890475 7.520000e-11 78.7
25 TraesCS6B01G049400 chr5A 91.228 57 1 3 2170 2224 329824395 329824449 9.730000e-10 75.0


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 TraesCS6B01G049400 chr6B 29059058 29061592 2534 True 4682.000 4682 100.00000 1 2535 1 chr6B.!!$R2 2534
1 TraesCS6B01G049400 chr6B 28925846 28926597 751 False 900.000 900 88.65700 807 1550 1 chr6B.!!$F1 743
2 TraesCS6B01G049400 chr6B 28256074 28256813 739 True 867.000 867 88.02600 807 1550 1 chr6B.!!$R1 743
3 TraesCS6B01G049400 chr6B 28977941 28981149 3208 True 604.850 1688 91.11150 1 2535 4 chr6B.!!$R3 2534
4 TraesCS6B01G049400 chr6D 16521802 16524172 2370 True 1215.000 2145 88.51950 1 2423 2 chr6D.!!$R1 2422
5 TraesCS6B01G049400 chr6D 16502655 16503450 795 False 998.000 998 89.33000 736 1535 1 chr6D.!!$F1 799
6 TraesCS6B01G049400 chr6A 16719436 16721180 1744 True 2039.000 2039 87.90800 1 1753 1 chr6A.!!$R3 1752
7 TraesCS6B01G049400 chr6A 16593229 16593984 755 True 909.000 909 88.70100 800 1550 1 chr6A.!!$R1 750
8 TraesCS6B01G049400 chr6A 16658124 16658878 754 True 874.000 874 87.99000 807 1550 1 chr6A.!!$R2 743
9 TraesCS6B01G049400 chr1B 587472429 587474581 2152 False 510.575 1380 88.32425 538 2535 4 chr1B.!!$F1 1997

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
410 417 0.107214 TCTAGCCAAATTGGAGCGGG 60.107 55.0 17.47 0.72 40.96 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 2179 0.540365 ATGTTTGCCCTCCTGTGTGG 60.54 55.0 0.0 0.0 37.1 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
78 79 5.087323 TGGAGCTCTTCTTCCTCTTTCTAA 58.913 41.667 14.64 0.00 0.00 2.10
82 83 7.609918 GGAGCTCTTCTTCCTCTTTCTAATTTT 59.390 37.037 14.64 0.00 0.00 1.82
110 111 6.206634 GGATCCGTTCTATCATTGCCAATTTA 59.793 38.462 0.00 0.00 0.00 1.40
112 113 6.119536 TCCGTTCTATCATTGCCAATTTACT 58.880 36.000 0.00 0.00 0.00 2.24
114 115 6.692681 CCGTTCTATCATTGCCAATTTACTTG 59.307 38.462 0.00 0.00 34.42 3.16
189 190 6.181206 ACTTCTAATATTGGAGGAGAAGCC 57.819 41.667 16.31 0.00 44.54 4.35
190 191 5.667626 ACTTCTAATATTGGAGGAGAAGCCA 59.332 40.000 16.31 0.00 44.54 4.75
208 209 2.403987 CGACAGACGGCTAGGTCG 59.596 66.667 15.69 15.69 45.62 4.79
256 262 3.399181 GGGGGCATGTGAGGACGA 61.399 66.667 0.00 0.00 0.00 4.20
296 302 2.675583 GGATTAAGGTCCCGGAGTAGT 58.324 52.381 0.73 0.00 31.82 2.73
299 305 4.468713 GATTAAGGTCCCGGAGTAGTAGT 58.531 47.826 0.73 0.00 0.00 2.73
361 367 0.331616 CGGTGGGGAAAAGAAGGGAT 59.668 55.000 0.00 0.00 0.00 3.85
371 377 6.776116 GGGGAAAAGAAGGGATAAATCGTTAT 59.224 38.462 0.00 0.00 32.36 1.89
383 389 4.600012 AAATCGTTATCCTTTGCACGAG 57.400 40.909 0.00 0.00 44.32 4.18
385 391 1.546923 TCGTTATCCTTTGCACGAGGA 59.453 47.619 17.81 17.81 46.73 3.71
393 399 3.012518 CCTTTGCACGAGGATGATTTCT 58.987 45.455 9.28 0.00 36.33 2.52
402 409 5.297776 CACGAGGATGATTTCTAGCCAAATT 59.702 40.000 0.00 0.00 0.00 1.82
404 411 5.278169 CGAGGATGATTTCTAGCCAAATTGG 60.278 44.000 7.84 7.84 41.55 3.16
408 415 3.378112 TGATTTCTAGCCAAATTGGAGCG 59.622 43.478 17.47 2.40 40.96 5.03
410 417 0.107214 TCTAGCCAAATTGGAGCGGG 60.107 55.000 17.47 0.72 40.96 6.13
416 423 0.677731 CAAATTGGAGCGGGAGAGCA 60.678 55.000 0.00 0.00 40.15 4.26
423 430 0.238553 GAGCGGGAGAGCACAAAAAC 59.761 55.000 0.00 0.00 40.15 2.43
432 439 1.299850 GCACAAAAACGTGGGAGGC 60.300 57.895 0.00 0.00 37.37 4.70
437 444 2.047213 AAAAACGTGGGAGGCCTCGA 62.047 55.000 26.36 12.85 0.00 4.04
468 476 2.653584 GCGATTTCATGCATGTATTCGC 59.346 45.455 36.54 36.54 43.73 4.70
530 539 5.162925 ACCGGATTGGAATTTGGGGAATATA 60.163 40.000 9.46 0.00 42.00 0.86
531 540 5.957774 CCGGATTGGAATTTGGGGAATATAT 59.042 40.000 0.00 0.00 42.00 0.86
532 541 7.122715 CCGGATTGGAATTTGGGGAATATATA 58.877 38.462 0.00 0.00 42.00 0.86
562 571 1.638529 TTTGGGGCCTTTGTACATGG 58.361 50.000 0.84 10.15 0.00 3.66
569 578 3.299503 GGCCTTTGTACATGGATCCAAT 58.700 45.455 20.67 12.85 0.00 3.16
642 658 4.479158 AGGGCTACATCTGAAAAACCAAA 58.521 39.130 0.00 0.00 0.00 3.28
670 688 8.510505 AGATGCAAGATAAGAGTGAAGAAAAAC 58.489 33.333 0.00 0.00 0.00 2.43
679 697 6.901081 AGAGTGAAGAAAAACCCTAAATGG 57.099 37.500 0.00 0.00 0.00 3.16
683 701 4.039852 TGAAGAAAAACCCTAAATGGTGCC 59.960 41.667 0.00 0.00 39.05 5.01
689 707 1.974957 ACCCTAAATGGTGCCCAAAAC 59.025 47.619 0.00 0.00 36.95 2.43
690 708 1.067213 CCCTAAATGGTGCCCAAAACG 60.067 52.381 0.00 0.00 36.95 3.60
691 709 1.889829 CCTAAATGGTGCCCAAAACGA 59.110 47.619 0.00 0.00 36.95 3.85
692 710 2.297597 CCTAAATGGTGCCCAAAACGAA 59.702 45.455 0.00 0.00 36.95 3.85
693 711 2.990066 AAATGGTGCCCAAAACGAAA 57.010 40.000 0.00 0.00 36.95 3.46
694 712 2.232756 AATGGTGCCCAAAACGAAAC 57.767 45.000 0.00 0.00 36.95 2.78
755 775 2.335092 ATCCCTGCGCTCTGATTGGG 62.335 60.000 9.73 8.80 36.14 4.12
984 1037 3.296709 TTTCCAGCTCGCCGGAGAC 62.297 63.158 5.05 2.21 43.27 3.36
1200 1254 2.582436 GCCGATCTTTCCCGTCCA 59.418 61.111 0.00 0.00 0.00 4.02
1537 1601 4.858680 GCCGCCAAGGAGTAGCCC 62.859 72.222 0.00 0.00 45.00 5.19
1538 1602 4.530857 CCGCCAAGGAGTAGCCCG 62.531 72.222 0.00 0.00 45.00 6.13
1629 1697 4.018870 TGGATCCTGTGTGTAATTGCCTAA 60.019 41.667 14.23 0.00 0.00 2.69
1646 1714 3.194968 GCCTAAGTCTGTAGTGGCTGTTA 59.805 47.826 0.00 0.00 37.58 2.41
1668 1736 3.370978 ACATTAGTTCGATGAACAAGCCG 59.629 43.478 11.81 0.00 44.11 5.52
1669 1737 2.004583 TAGTTCGATGAACAAGCCGG 57.995 50.000 11.81 0.00 44.11 6.13
1671 1739 1.274167 AGTTCGATGAACAAGCCGGTA 59.726 47.619 1.90 0.00 44.11 4.02
1672 1740 1.659098 GTTCGATGAACAAGCCGGTAG 59.341 52.381 1.90 0.00 41.62 3.18
1673 1741 1.179152 TCGATGAACAAGCCGGTAGA 58.821 50.000 1.90 0.00 0.00 2.59
1674 1742 1.754803 TCGATGAACAAGCCGGTAGAT 59.245 47.619 1.90 0.00 0.00 1.98
1675 1743 1.860950 CGATGAACAAGCCGGTAGATG 59.139 52.381 1.90 0.00 0.00 2.90
1676 1744 2.213499 GATGAACAAGCCGGTAGATGG 58.787 52.381 1.90 0.00 0.00 3.51
1677 1745 0.251916 TGAACAAGCCGGTAGATGGG 59.748 55.000 1.90 0.00 0.00 4.00
1808 1912 8.396272 ACTGTCAGCTTCTTGTTATTAACATT 57.604 30.769 9.95 0.00 41.79 2.71
1809 1913 8.292448 ACTGTCAGCTTCTTGTTATTAACATTG 58.708 33.333 9.95 6.85 41.79 2.82
1810 1914 7.592938 TGTCAGCTTCTTGTTATTAACATTGG 58.407 34.615 9.95 4.71 41.79 3.16
1811 1915 7.446931 TGTCAGCTTCTTGTTATTAACATTGGA 59.553 33.333 9.95 6.67 41.79 3.53
1814 1918 9.941664 CAGCTTCTTGTTATTAACATTGGATAG 57.058 33.333 9.95 4.14 41.79 2.08
1815 1919 9.686683 AGCTTCTTGTTATTAACATTGGATAGT 57.313 29.630 9.95 0.00 41.79 2.12
1816 1920 9.937175 GCTTCTTGTTATTAACATTGGATAGTC 57.063 33.333 9.95 0.00 41.79 2.59
1859 1989 7.482169 AGATACTCCTGAGTTACAAACATGA 57.518 36.000 4.94 0.00 42.54 3.07
1904 2059 6.243148 TGTAGTCAGATGTACCTAACAGACA 58.757 40.000 0.00 0.00 42.70 3.41
1946 2115 9.753674 AAATGAGATACCAGAATTACTTTTGGA 57.246 29.630 9.10 0.00 34.76 3.53
1950 2119 7.918076 AGATACCAGAATTACTTTTGGACTGA 58.082 34.615 9.10 0.00 34.76 3.41
2001 2179 3.935203 TGCTACTGTAGAAGAATGCTTGC 59.065 43.478 18.64 0.08 33.61 4.01
2002 2180 3.311048 GCTACTGTAGAAGAATGCTTGCC 59.689 47.826 18.64 0.00 33.61 4.52
2003 2181 3.423539 ACTGTAGAAGAATGCTTGCCA 57.576 42.857 0.00 0.00 33.61 4.92
2018 2198 2.564721 GCCACACAGGAGGGCAAAC 61.565 63.158 0.00 0.00 46.92 2.93
2066 2249 4.067192 TGCTGCGCTTCATGTATCAATAT 58.933 39.130 9.73 0.00 0.00 1.28
2138 2329 7.362056 CCACTGTGGAGAAAATAACAGGTAATG 60.362 40.741 22.33 0.00 43.45 1.90
2158 2349 7.118680 GGTAATGATCTCAGTAAAACGGTGAAA 59.881 37.037 0.00 0.00 0.00 2.69
2179 2370 7.907389 TGAAATAGTCAGAGGTTTCACATAGT 58.093 34.615 0.00 0.00 36.11 2.12
2180 2371 7.819415 TGAAATAGTCAGAGGTTTCACATAGTG 59.181 37.037 0.00 0.00 36.11 2.74
2181 2372 3.931578 AGTCAGAGGTTTCACATAGTGC 58.068 45.455 0.00 0.00 32.98 4.40
2182 2373 3.003480 GTCAGAGGTTTCACATAGTGCC 58.997 50.000 0.00 0.00 32.98 5.01
2183 2374 2.637382 TCAGAGGTTTCACATAGTGCCA 59.363 45.455 0.00 0.00 32.98 4.92
2184 2375 3.072330 TCAGAGGTTTCACATAGTGCCAA 59.928 43.478 0.00 0.00 32.98 4.52
2209 2400 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
2210 2401 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
2211 2402 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
2212 2403 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2213 2404 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2214 2405 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2256 2852 5.237815 CCCCTTTCTCTTTTACATTTTGCC 58.762 41.667 0.00 0.00 0.00 4.52
2313 2911 7.978414 GCTATCATCAGAATACAGCTAAGCATA 59.022 37.037 0.00 0.00 0.00 3.14
2449 3108 2.409948 TTGTTTGCCCACCCTTTTTG 57.590 45.000 0.00 0.00 0.00 2.44
2450 3109 1.280457 TGTTTGCCCACCCTTTTTGT 58.720 45.000 0.00 0.00 0.00 2.83
2499 3446 8.110271 TCTATATGACTGTATCTTACTCCCCTG 58.890 40.741 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.863809 AGAACAAATCTTGGGAAGCGT 58.136 42.857 0.00 0.00 33.39 5.07
82 83 3.882888 GGCAATGATAGAACGGATCCAAA 59.117 43.478 13.41 0.00 0.00 3.28
84 85 2.437651 TGGCAATGATAGAACGGATCCA 59.562 45.455 13.41 0.00 0.00 3.41
163 164 7.202011 GGCTTCTCCTCCAATATTAGAAGTACA 60.202 40.741 19.18 0.00 43.21 2.90
189 190 1.136984 GACCTAGCCGTCTGTCGTG 59.863 63.158 0.00 0.00 37.94 4.35
190 191 2.396955 CGACCTAGCCGTCTGTCGT 61.397 63.158 8.31 0.00 44.00 4.34
222 223 3.784311 CCCCCATCTCCTCCTCATATA 57.216 52.381 0.00 0.00 0.00 0.86
248 254 2.687805 CGGCTCGTTCTCGTCCTCA 61.688 63.158 0.00 0.00 38.33 3.86
256 262 4.755614 GACGTCGCGGCTCGTTCT 62.756 66.667 20.61 4.18 40.39 3.01
281 287 2.174424 CCTACTACTACTCCGGGACCTT 59.826 54.545 0.00 0.00 0.00 3.50
296 302 2.932736 CCGGCCCTCCTCCTACTA 59.067 66.667 0.00 0.00 0.00 1.82
344 350 4.338400 CGATTTATCCCTTCTTTTCCCCAC 59.662 45.833 0.00 0.00 0.00 4.61
361 367 4.569162 CCTCGTGCAAAGGATAACGATTTA 59.431 41.667 10.29 0.00 43.39 1.40
371 377 2.787473 AATCATCCTCGTGCAAAGGA 57.213 45.000 18.69 18.69 46.68 3.36
383 389 5.508657 GCTCCAATTTGGCTAGAAATCATCC 60.509 44.000 10.76 0.00 37.47 3.51
385 391 4.037208 CGCTCCAATTTGGCTAGAAATCAT 59.963 41.667 10.76 0.00 37.47 2.45
386 392 3.378112 CGCTCCAATTTGGCTAGAAATCA 59.622 43.478 10.76 0.00 37.47 2.57
387 393 3.243201 CCGCTCCAATTTGGCTAGAAATC 60.243 47.826 10.76 0.00 37.47 2.17
389 395 2.091541 CCGCTCCAATTTGGCTAGAAA 58.908 47.619 10.76 0.00 37.47 2.52
393 399 0.107214 CTCCCGCTCCAATTTGGCTA 60.107 55.000 10.76 0.00 37.47 3.93
402 409 2.050836 TTTTGTGCTCTCCCGCTCCA 62.051 55.000 0.00 0.00 0.00 3.86
404 411 0.238553 GTTTTTGTGCTCTCCCGCTC 59.761 55.000 0.00 0.00 0.00 5.03
408 415 0.310854 CCACGTTTTTGTGCTCTCCC 59.689 55.000 0.00 0.00 38.55 4.30
410 417 1.264288 CTCCCACGTTTTTGTGCTCTC 59.736 52.381 0.00 0.00 38.55 3.20
416 423 0.822121 GAGGCCTCCCACGTTTTTGT 60.822 55.000 23.19 0.00 0.00 2.83
423 430 3.827898 GTCTCGAGGCCTCCCACG 61.828 72.222 27.20 16.19 45.09 4.94
432 439 1.983196 ATCGCTCACACGTCTCGAGG 61.983 60.000 13.56 0.00 32.50 4.63
437 444 1.995484 CATGAAATCGCTCACACGTCT 59.005 47.619 0.00 0.00 0.00 4.18
562 571 7.360438 GCTGTTATCTAACGATTGGATTGGATC 60.360 40.741 0.00 0.00 39.00 3.36
569 578 6.428465 TGTTTTGCTGTTATCTAACGATTGGA 59.572 34.615 0.00 0.00 39.00 3.53
574 584 5.462729 TCGTTGTTTTGCTGTTATCTAACGA 59.537 36.000 0.00 0.00 43.09 3.85
621 631 4.864704 TTTGGTTTTTCAGATGTAGCCC 57.135 40.909 0.00 0.00 0.00 5.19
622 632 7.391148 TCTATTTGGTTTTTCAGATGTAGCC 57.609 36.000 0.00 0.00 0.00 3.93
623 636 7.433425 GCATCTATTTGGTTTTTCAGATGTAGC 59.567 37.037 10.18 0.00 40.82 3.58
642 658 9.896645 TTTTCTTCACTCTTATCTTGCATCTAT 57.103 29.630 0.00 0.00 0.00 1.98
679 697 1.910688 TTTCGTTTCGTTTTGGGCAC 58.089 45.000 0.00 0.00 0.00 5.01
683 701 2.855370 CCTGGTTTTCGTTTCGTTTTGG 59.145 45.455 0.00 0.00 0.00 3.28
689 707 2.836479 AACACCTGGTTTTCGTTTCG 57.164 45.000 0.00 0.00 35.82 3.46
690 708 8.631676 TTTAATTAACACCTGGTTTTCGTTTC 57.368 30.769 0.67 0.00 40.96 2.78
691 709 7.223193 GCTTTAATTAACACCTGGTTTTCGTTT 59.777 33.333 0.67 0.00 40.96 3.60
692 710 6.698329 GCTTTAATTAACACCTGGTTTTCGTT 59.302 34.615 0.67 3.62 40.96 3.85
693 711 6.183360 TGCTTTAATTAACACCTGGTTTTCGT 60.183 34.615 0.67 0.00 40.96 3.85
694 712 6.210078 TGCTTTAATTAACACCTGGTTTTCG 58.790 36.000 0.67 0.00 40.96 3.46
758 778 3.698263 ATCCGGGGGAGGGTCTGAC 62.698 68.421 0.00 0.00 34.05 3.51
771 791 4.418328 TTTGGGGGTGCGATCCGG 62.418 66.667 0.00 0.00 0.00 5.14
984 1037 0.179171 CCATCTTCTTGCTTGCTGCG 60.179 55.000 0.00 0.00 46.63 5.18
1345 1406 3.220999 CTCCTGGTCGTTGCGGACA 62.221 63.158 0.00 0.00 38.70 4.02
1537 1601 1.022735 ACGACAGTAGTCTATGGGCG 58.977 55.000 7.27 7.27 42.73 6.13
1538 1602 2.022195 TCACGACAGTAGTCTATGGGC 58.978 52.381 0.00 0.00 42.73 5.36
1629 1697 4.891992 AATGTAACAGCCACTACAGACT 57.108 40.909 0.00 0.00 31.81 3.24
1646 1714 3.370978 CGGCTTGTTCATCGAACTAATGT 59.629 43.478 8.23 0.00 42.39 2.71
1668 1736 2.256117 AATTACAGCGCCCATCTACC 57.744 50.000 2.29 0.00 0.00 3.18
1669 1737 5.238583 AGATAAATTACAGCGCCCATCTAC 58.761 41.667 2.29 0.00 0.00 2.59
1671 1739 4.040952 AGAGATAAATTACAGCGCCCATCT 59.959 41.667 2.29 0.46 0.00 2.90
1672 1740 4.153117 CAGAGATAAATTACAGCGCCCATC 59.847 45.833 2.29 0.00 0.00 3.51
1673 1741 4.067896 CAGAGATAAATTACAGCGCCCAT 58.932 43.478 2.29 0.00 0.00 4.00
1674 1742 3.133901 TCAGAGATAAATTACAGCGCCCA 59.866 43.478 2.29 0.00 0.00 5.36
1675 1743 3.728845 TCAGAGATAAATTACAGCGCCC 58.271 45.455 2.29 0.00 0.00 6.13
1676 1744 5.931441 AATCAGAGATAAATTACAGCGCC 57.069 39.130 2.29 0.00 0.00 6.53
1677 1745 8.499162 ACATAAATCAGAGATAAATTACAGCGC 58.501 33.333 0.00 0.00 0.00 5.92
1855 1984 5.697178 TGATTTTGTCATTTGCCTTGTCATG 59.303 36.000 0.00 0.00 0.00 3.07
1859 1989 5.613329 ACATGATTTTGTCATTTGCCTTGT 58.387 33.333 0.00 0.00 45.25 3.16
1946 2115 6.069331 TCTCAGTAAGTACCTGTTTCTCAGT 58.931 40.000 0.00 0.00 42.19 3.41
1950 2119 7.963532 TGATTTCTCAGTAAGTACCTGTTTCT 58.036 34.615 0.00 0.00 0.00 2.52
2001 2179 0.540365 ATGTTTGCCCTCCTGTGTGG 60.540 55.000 0.00 0.00 37.10 4.17
2002 2180 1.000060 CAATGTTTGCCCTCCTGTGTG 60.000 52.381 0.00 0.00 0.00 3.82
2003 2181 1.331214 CAATGTTTGCCCTCCTGTGT 58.669 50.000 0.00 0.00 0.00 3.72
2018 2198 7.864686 TCGACTTGATTATTTATCCAGCAATG 58.135 34.615 0.00 0.00 30.87 2.82
2138 2329 7.544566 TGACTATTTCACCGTTTTACTGAGATC 59.455 37.037 0.00 0.00 0.00 2.75
2158 2349 5.395768 GGCACTATGTGAAACCTCTGACTAT 60.396 44.000 1.52 0.00 35.23 2.12
2184 2375 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
2190 2381 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
2191 2382 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2192 2383 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2193 2384 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2194 2385 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2195 2386 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2196 2387 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2197 2388 3.339713 TTACTCCCTCCGTCCCATAAT 57.660 47.619 0.00 0.00 0.00 1.28
2198 2389 2.852714 TTACTCCCTCCGTCCCATAA 57.147 50.000 0.00 0.00 0.00 1.90
2199 2390 4.140853 ACTTATTACTCCCTCCGTCCCATA 60.141 45.833 0.00 0.00 0.00 2.74
2200 2391 3.240302 CTTATTACTCCCTCCGTCCCAT 58.760 50.000 0.00 0.00 0.00 4.00
2201 2392 2.023695 ACTTATTACTCCCTCCGTCCCA 60.024 50.000 0.00 0.00 0.00 4.37
2202 2393 2.675583 ACTTATTACTCCCTCCGTCCC 58.324 52.381 0.00 0.00 0.00 4.46
2203 2394 4.462132 GGATACTTATTACTCCCTCCGTCC 59.538 50.000 0.00 0.00 0.00 4.79
2204 2395 4.462132 GGGATACTTATTACTCCCTCCGTC 59.538 50.000 0.00 0.00 43.45 4.79
2205 2396 4.414677 GGGATACTTATTACTCCCTCCGT 58.585 47.826 0.00 0.00 43.45 4.69
2210 2401 5.280062 GGCAAGAGGGATACTTATTACTCCC 60.280 48.000 0.00 0.00 46.56 4.30
2211 2402 5.280062 GGGCAAGAGGGATACTTATTACTCC 60.280 48.000 0.00 0.00 0.00 3.85
2212 2403 5.280062 GGGGCAAGAGGGATACTTATTACTC 60.280 48.000 0.00 0.00 0.00 2.59
2213 2404 4.597940 GGGGCAAGAGGGATACTTATTACT 59.402 45.833 0.00 0.00 0.00 2.24
2214 2405 4.597940 AGGGGCAAGAGGGATACTTATTAC 59.402 45.833 0.00 0.00 0.00 1.89
2256 2852 2.300152 TGAGAGCAGAGTTACAGTTGGG 59.700 50.000 0.00 0.00 0.00 4.12
2313 2911 4.218417 GGTTAGAAGTTGATGTGCATTGGT 59.782 41.667 0.00 0.00 0.00 3.67
2321 2919 5.564550 AGATGCAAGGTTAGAAGTTGATGT 58.435 37.500 0.00 0.00 0.00 3.06
2418 3017 6.172630 GGTGGGCAAACAAAAATATGAGAAT 58.827 36.000 0.00 0.00 0.00 2.40
2429 3088 2.040412 ACAAAAAGGGTGGGCAAACAAA 59.960 40.909 0.00 0.00 0.00 2.83
2449 3108 5.542779 AGACATGTCTAAGGTTCAGTTCAC 58.457 41.667 26.87 0.00 38.35 3.18
2450 3109 5.808366 AGACATGTCTAAGGTTCAGTTCA 57.192 39.130 26.87 0.00 38.35 3.18
2499 3446 1.038280 ATCGAGACGATGGGGGTAAC 58.962 55.000 5.86 0.00 45.24 2.50


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

AutoCloner maintained by Alex Coulton.