Multiple sequence alignment - TraesCS2A01G378900

Loading Multiple Alignment...

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 TraesCS2A01G378900 chr2A 100.000 3032 0 0 1 3032 621568001 621564970 0.000000e+00 5600
1 TraesCS2A01G378900 chr2D 92.355 1478 77 14 1558 3032 478874135 478872691 0.000000e+00 2071
2 TraesCS2A01G378900 chr2D 88.840 1595 119 28 15 1561 478875874 478874291 0.000000e+00 1905
3 TraesCS2A01G378900 chr2B 88.938 1582 118 24 19 1561 561284791 561283228 0.000000e+00 1899
4 TraesCS2A01G378900 chr2B 91.127 710 34 7 1558 2261 561283106 561282420 0.000000e+00 935
5 TraesCS2A01G378900 chr2B 85.249 522 38 8 2346 2864 561282410 561281925 4.510000e-138 501
6 TraesCS2A01G378900 chr2B 96.491 171 5 1 2863 3032 561281842 561281672 6.400000e-72 281


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 TraesCS2A01G378900 chr2A 621564970 621568001 3031 True 5600 5600 100.00000 1 3032 1 chr2A.!!$R1 3031
1 TraesCS2A01G378900 chr2D 478872691 478875874 3183 True 1988 2071 90.59750 15 3032 2 chr2D.!!$R1 3017
2 TraesCS2A01G378900 chr2B 561281672 561284791 3119 True 904 1899 90.45125 19 3032 4 chr2B.!!$R1 3013

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
97 98 0.172803 ACGCGTAACTGCCTTAGAGG 59.827 55.0 11.67 0.0 38.80 3.69 F
468 496 0.178068 TGATCTTTCCTGCTACCGGC 59.822 55.0 0.00 0.0 42.22 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1348 1389 0.549950 AGGGCATCCATGAACTCCAG 59.450 55.0 0.00 0.0 34.83 3.86 R
2117 2331 0.111253 CCCTCATGTTGGCCTATCCC 59.889 60.0 3.32 0.0 0.00 3.85 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
77 78 6.915544 TCTGAAGATGCACATAAGATGAAC 57.084 37.500 0.00 0.00 0.00 3.18
79 80 6.314648 TCTGAAGATGCACATAAGATGAACAC 59.685 38.462 0.00 0.00 0.00 3.32
81 82 3.310774 AGATGCACATAAGATGAACACGC 59.689 43.478 0.00 0.00 0.00 5.34
88 89 4.326278 ACATAAGATGAACACGCGTAACTG 59.674 41.667 13.44 1.07 0.00 3.16
92 93 0.531090 TGAACACGCGTAACTGCCTT 60.531 50.000 13.44 0.00 0.00 4.35
94 95 1.389106 GAACACGCGTAACTGCCTTAG 59.611 52.381 13.44 0.00 0.00 2.18
96 97 1.269166 CACGCGTAACTGCCTTAGAG 58.731 55.000 13.44 0.00 0.00 2.43
97 98 0.172803 ACGCGTAACTGCCTTAGAGG 59.827 55.000 11.67 0.00 38.80 3.69
121 128 1.900545 AACTACCGCTGGGCTCTTCC 61.901 60.000 0.00 0.00 36.48 3.46
138 145 4.082845 TCTTCCGGGATAGCTTCTCATAG 58.917 47.826 0.00 0.00 0.00 2.23
200 207 9.342308 GATATCATTGTCTGGATAAAAAGGACA 57.658 33.333 0.00 0.00 35.51 4.02
228 235 5.537300 AAGATATTCCGAGCTTTAGCAGA 57.463 39.130 4.33 0.00 45.16 4.26
303 310 6.708949 TGTTTTTAGGAATACACGAGAAAGCT 59.291 34.615 0.00 0.00 0.00 3.74
309 316 5.185249 AGGAATACACGAGAAAGCTCACTTA 59.815 40.000 0.00 0.00 41.36 2.24
310 317 5.288952 GGAATACACGAGAAAGCTCACTTAC 59.711 44.000 0.00 0.00 41.36 2.34
319 347 7.042658 ACGAGAAAGCTCACTTACTTAAAACAG 60.043 37.037 0.00 0.00 41.36 3.16
321 349 8.144155 AGAAAGCTCACTTACTTAAAACAGAC 57.856 34.615 0.00 0.00 34.05 3.51
350 378 7.675403 GCATATTCTTTGCATGTTCAAATGTGG 60.675 37.037 0.00 0.00 39.90 4.17
352 380 5.471556 TCTTTGCATGTTCAAATGTGGAT 57.528 34.783 0.00 0.00 35.64 3.41
354 382 6.990798 TCTTTGCATGTTCAAATGTGGATTA 58.009 32.000 0.00 0.00 35.64 1.75
359 387 8.291191 TGCATGTTCAAATGTGGATTATCTTA 57.709 30.769 0.00 0.00 0.00 2.10
360 388 8.916062 TGCATGTTCAAATGTGGATTATCTTAT 58.084 29.630 0.00 0.00 0.00 1.73
372 400 9.109393 TGTGGATTATCTTATTAGTGAAAGTGC 57.891 33.333 0.00 0.00 0.00 4.40
385 413 6.795098 AGTGAAAGTGCGTGTATTGAATTA 57.205 33.333 0.00 0.00 0.00 1.40
389 417 8.911662 GTGAAAGTGCGTGTATTGAATTATTTT 58.088 29.630 0.00 0.00 0.00 1.82
390 418 9.469807 TGAAAGTGCGTGTATTGAATTATTTTT 57.530 25.926 0.00 0.00 0.00 1.94
441 469 2.122768 CTAATCTCTTGGCCCACTCCT 58.877 52.381 0.00 0.00 0.00 3.69
443 471 2.503869 ATCTCTTGGCCCACTCCTAT 57.496 50.000 0.00 0.00 0.00 2.57
458 486 6.229733 CCACTCCTATGATTCTGATCTTTCC 58.770 44.000 0.00 0.00 33.28 3.13
463 491 6.784473 TCCTATGATTCTGATCTTTCCTGCTA 59.216 38.462 0.00 0.00 33.28 3.49
466 494 3.526931 TTCTGATCTTTCCTGCTACCG 57.473 47.619 0.00 0.00 0.00 4.02
468 496 0.178068 TGATCTTTCCTGCTACCGGC 59.822 55.000 0.00 0.00 42.22 6.13
488 517 6.593770 ACCGGCCATTGAATTTTTATTCTTTC 59.406 34.615 0.00 0.00 0.00 2.62
491 520 6.883756 GGCCATTGAATTTTTATTCTTTCCCA 59.116 34.615 0.00 0.00 0.00 4.37
502 531 7.873719 TTTATTCTTTCCCAGCGAATTGATA 57.126 32.000 0.00 0.00 0.00 2.15
567 596 6.089820 GCATATTGAGTTGTTGTTGTCATTGG 59.910 38.462 0.00 0.00 0.00 3.16
574 603 3.779759 TGTTGTTGTCATTGGTTGCTTC 58.220 40.909 0.00 0.00 0.00 3.86
582 611 4.644234 TGTCATTGGTTGCTTCAGAGAAAA 59.356 37.500 0.00 0.00 0.00 2.29
608 639 2.496899 AGACTTATGGTTGGCTGGTG 57.503 50.000 0.00 0.00 0.00 4.17
632 663 8.610035 GTGGCAGGAGTTTAGTTGTATTAATAC 58.390 37.037 17.18 17.18 0.00 1.89
653 684 5.019785 ACGACTACCCTCATAAATTGTCC 57.980 43.478 0.00 0.00 0.00 4.02
702 733 1.548357 GCCACCTCTCTTGCTCTCCA 61.548 60.000 0.00 0.00 0.00 3.86
738 769 3.482436 CAAGGCACCTGTTACCTAAACA 58.518 45.455 0.00 0.00 45.90 2.83
749 780 6.715264 CCTGTTACCTAAACATGTCCTCTTTT 59.285 38.462 0.00 0.00 46.81 2.27
846 880 1.005630 GTCGACACCTGCTGCTTCT 60.006 57.895 11.55 0.00 0.00 2.85
862 896 5.048434 GCTGCTTCTTTAGTGTCCAAGAATT 60.048 40.000 0.00 0.00 38.15 2.17
899 937 2.630889 TCTCCTTCATGTGTCCTCCT 57.369 50.000 0.00 0.00 0.00 3.69
906 944 2.248248 TCATGTGTCCTCCTCTCGTTT 58.752 47.619 0.00 0.00 0.00 3.60
919 957 5.507637 TCCTCTCGTTTCTGAATACTACCT 58.492 41.667 0.00 0.00 0.00 3.08
1056 1094 0.527565 GGATCAACAACTGCGCCATT 59.472 50.000 4.18 0.00 0.00 3.16
1068 1106 0.371645 GCGCCATTGAACTCTTCTCG 59.628 55.000 0.00 0.00 0.00 4.04
1069 1107 0.371645 CGCCATTGAACTCTTCTCGC 59.628 55.000 0.00 0.00 0.00 5.03
1307 1348 2.542411 CGGCTCAAAGCATGCCTTATTC 60.542 50.000 15.66 0.00 44.75 1.75
1319 1360 5.759273 GCATGCCTTATTCCATTGCAAATTA 59.241 36.000 6.36 0.00 35.30 1.40
1326 1367 9.550406 CCTTATTCCATTGCAAATTAACATGAT 57.450 29.630 1.71 0.00 0.00 2.45
1352 1393 8.536175 TGAATCATACATACACAAGTTACTGGA 58.464 33.333 0.00 0.00 0.00 3.86
1373 1414 3.294214 AGTTCATGGATGCCCTTGATTC 58.706 45.455 0.00 0.00 43.50 2.52
1406 1447 3.545724 TGCCTCAGCATCTCAAGTG 57.454 52.632 0.00 0.00 46.52 3.16
1417 1458 8.846943 TCAGCATCTCAAGTGAACTTAATTTA 57.153 30.769 0.00 0.00 34.28 1.40
1446 1494 6.042777 TGCGTCCTAAGAGACAGATTATTTG 58.957 40.000 0.00 0.00 36.52 2.32
1684 1892 1.597663 GGCGGAAGTTGTTATGGATCG 59.402 52.381 0.00 0.00 0.00 3.69
1689 1897 3.621715 GGAAGTTGTTATGGATCGTGACC 59.378 47.826 0.00 0.00 0.00 4.02
1836 2044 0.585838 CAAAATGGTTGTTTGGCGGC 59.414 50.000 0.00 0.00 33.25 6.53
1838 2046 1.333177 AAATGGTTGTTTGGCGGCTA 58.667 45.000 11.43 0.00 0.00 3.93
1842 2050 0.039527 GGTTGTTTGGCGGCTACTTG 60.040 55.000 11.43 0.00 0.00 3.16
1869 2077 4.085357 ACGATCTGGGCAATTTAGCATA 57.915 40.909 0.00 0.00 35.83 3.14
1872 2080 6.237901 ACGATCTGGGCAATTTAGCATAATA 58.762 36.000 0.00 0.00 35.83 0.98
1873 2081 6.149474 ACGATCTGGGCAATTTAGCATAATAC 59.851 38.462 0.00 0.00 35.83 1.89
1874 2082 6.372659 CGATCTGGGCAATTTAGCATAATACT 59.627 38.462 0.00 0.00 35.83 2.12
1875 2083 6.882610 TCTGGGCAATTTAGCATAATACTG 57.117 37.500 0.00 0.00 35.83 2.74
1880 2088 7.723616 TGGGCAATTTAGCATAATACTGTATGT 59.276 33.333 0.22 0.00 34.51 2.29
1954 2162 1.004440 GTGAAGGACAGAAGCGCCT 60.004 57.895 2.29 0.00 0.00 5.52
2007 2215 0.892755 ATGTTCTTCGCGAGGTGGTA 59.107 50.000 18.33 4.13 0.00 3.25
2072 2286 1.093159 GCTGTTTGATCTGGGAGCTG 58.907 55.000 0.00 0.00 0.00 4.24
2077 2291 2.110627 GATCTGGGAGCTGCGCAT 59.889 61.111 12.24 0.00 38.89 4.73
2117 2331 5.855740 TTACCCAAAAACCTGTACAAAGG 57.144 39.130 0.00 0.00 43.57 3.11
2137 2351 1.140312 GGATAGGCCAACATGAGGGA 58.860 55.000 5.01 0.00 36.34 4.20
2138 2352 1.494721 GGATAGGCCAACATGAGGGAA 59.505 52.381 5.01 0.00 36.34 3.97
2139 2353 2.091885 GGATAGGCCAACATGAGGGAAA 60.092 50.000 5.01 0.00 36.34 3.13
2140 2354 2.507407 TAGGCCAACATGAGGGAAAC 57.493 50.000 5.01 0.00 0.00 2.78
2261 2475 6.805713 AGGTGTTCCTGTCAAGTTTATTTTG 58.194 36.000 0.00 0.00 43.33 2.44
2274 2488 9.921637 TCAAGTTTATTTTGTTTTCAGTTCTGT 57.078 25.926 0.00 0.00 0.00 3.41
2319 2533 2.638363 GGTAAAAGACCTCCTGGAGTGT 59.362 50.000 21.70 18.06 45.89 3.55
2351 2565 0.606673 GGGCTCGCTTCCTGTTTCTT 60.607 55.000 0.00 0.00 0.00 2.52
2376 2591 0.452987 AAGGCACATTGCTGCGTATG 59.547 50.000 11.53 11.53 44.28 2.39
2402 2618 2.243957 CGTGAAGCTGGCGTGTTCA 61.244 57.895 0.00 0.00 0.00 3.18
2403 2619 1.279840 GTGAAGCTGGCGTGTTCAC 59.720 57.895 9.12 9.12 42.31 3.18
2405 2621 0.391228 TGAAGCTGGCGTGTTCACTA 59.609 50.000 0.00 0.00 0.00 2.74
2422 2638 5.950544 TCACTAGGTATACCTTGCATTGT 57.049 39.130 29.09 14.83 46.09 2.71
2449 2665 4.692475 CGTTCGGGGCCTTTCCGT 62.692 66.667 17.11 0.00 46.82 4.69
2450 2666 3.053896 GTTCGGGGCCTTTCCGTG 61.054 66.667 17.11 0.00 46.82 4.94
2452 2668 2.598787 TTCGGGGCCTTTCCGTGAT 61.599 57.895 17.11 0.00 46.82 3.06
2477 2693 2.556189 ACAATGCAATGCCTTCACGTTA 59.444 40.909 1.53 0.00 0.00 3.18
2580 2799 0.318441 TGCTGACCTTCCTCTTGACG 59.682 55.000 0.00 0.00 0.00 4.35
2599 2818 4.751600 TGACGCTGAATGTGGATATTCATC 59.248 41.667 0.00 0.00 43.80 2.92
2651 2871 6.883217 AGTCTGCAATAGTCAATCAATCAACT 59.117 34.615 0.00 0.00 0.00 3.16
2654 2874 8.024865 TCTGCAATAGTCAATCAATCAACTTTG 58.975 33.333 0.00 0.00 0.00 2.77
2767 2987 6.522946 TCTCTCATCTATTCTGCATTTCAGG 58.477 40.000 0.00 0.00 43.06 3.86
2786 3006 9.607333 ATTTCAGGAGATCTATGTCAACCTATA 57.393 33.333 0.00 0.00 0.00 1.31
2803 3023 9.100197 TCAACCTATATCACAGGATAATAGCAA 57.900 33.333 0.00 0.00 39.36 3.91
2835 3055 3.885724 TCATCTGAAACCTATGTCGCA 57.114 42.857 0.00 0.00 0.00 5.10
2960 3265 2.505407 TGGTACAAGATCCACATGGAGG 59.495 50.000 6.77 0.00 41.98 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.096695 GCAAAAGTGTGACAGGTAAGAAAAA 58.903 36.000 0.00 0.00 0.00 1.94
11 12 5.184096 TGCAAAAGTGTGACAGGTAAGAAAA 59.816 36.000 0.00 0.00 0.00 2.29
12 13 4.702612 TGCAAAAGTGTGACAGGTAAGAAA 59.297 37.500 0.00 0.00 0.00 2.52
13 14 4.265893 TGCAAAAGTGTGACAGGTAAGAA 58.734 39.130 0.00 0.00 0.00 2.52
14 15 3.879998 TGCAAAAGTGTGACAGGTAAGA 58.120 40.909 0.00 0.00 0.00 2.10
15 16 4.630894 TTGCAAAAGTGTGACAGGTAAG 57.369 40.909 0.00 0.00 0.00 2.34
16 17 5.278266 GCTATTGCAAAAGTGTGACAGGTAA 60.278 40.000 1.71 0.00 39.41 2.85
17 18 4.215399 GCTATTGCAAAAGTGTGACAGGTA 59.785 41.667 1.71 0.00 39.41 3.08
61 62 2.030823 CGCGTGTTCATCTTATGTGCAT 59.969 45.455 0.00 0.00 0.00 3.96
77 78 1.269166 CTCTAAGGCAGTTACGCGTG 58.731 55.000 24.59 5.95 0.00 5.34
79 80 2.959275 CCTCTAAGGCAGTTACGCG 58.041 57.895 3.53 3.53 0.00 6.01
92 93 2.429610 CCAGCGGTAGTTTTAGCCTCTA 59.570 50.000 0.00 0.00 0.00 2.43
94 95 1.653151 CCAGCGGTAGTTTTAGCCTC 58.347 55.000 0.00 0.00 0.00 4.70
96 97 1.374343 GCCCAGCGGTAGTTTTAGCC 61.374 60.000 0.00 0.00 0.00 3.93
97 98 0.392595 AGCCCAGCGGTAGTTTTAGC 60.393 55.000 0.00 0.00 0.00 3.09
98 99 1.207329 AGAGCCCAGCGGTAGTTTTAG 59.793 52.381 0.00 0.00 0.00 1.85
99 100 1.272807 AGAGCCCAGCGGTAGTTTTA 58.727 50.000 0.00 0.00 0.00 1.52
101 102 0.036294 GAAGAGCCCAGCGGTAGTTT 60.036 55.000 0.00 0.00 0.00 2.66
102 103 1.597461 GAAGAGCCCAGCGGTAGTT 59.403 57.895 0.00 0.00 0.00 2.24
103 104 2.359967 GGAAGAGCCCAGCGGTAGT 61.360 63.158 0.00 0.00 0.00 2.73
104 105 2.501610 GGAAGAGCCCAGCGGTAG 59.498 66.667 0.00 0.00 0.00 3.18
105 106 3.458163 CGGAAGAGCCCAGCGGTA 61.458 66.667 0.00 0.00 0.00 4.02
173 180 9.566432 GTCCTTTTTATCCAGACAATGATATCT 57.434 33.333 3.98 0.00 0.00 1.98
200 207 9.120538 TGCTAAAGCTCGGAATATCTTTAAAAT 57.879 29.630 3.26 0.00 42.66 1.82
207 214 4.557695 CGTCTGCTAAAGCTCGGAATATCT 60.558 45.833 3.26 0.00 42.66 1.98
213 220 0.452184 CTCGTCTGCTAAAGCTCGGA 59.548 55.000 3.26 0.00 42.66 4.55
261 268 8.356657 CCTAAAAACAATTGTACAGAACATCCA 58.643 33.333 12.39 0.00 38.10 3.41
290 297 5.449107 AAGTAAGTGAGCTTTCTCGTGTA 57.551 39.130 0.00 0.00 42.26 2.90
310 317 9.495754 GCAAAGAATATGCTAGTCTGTTTTAAG 57.504 33.333 0.00 0.00 40.64 1.85
319 347 7.019774 TGAACATGCAAAGAATATGCTAGTC 57.980 36.000 0.00 0.00 44.14 2.59
321 349 8.752254 CATTTGAACATGCAAAGAATATGCTAG 58.248 33.333 0.00 0.00 44.14 3.42
334 362 6.778834 AGATAATCCACATTTGAACATGCA 57.221 33.333 0.00 0.00 0.00 3.96
335 363 9.754382 AATAAGATAATCCACATTTGAACATGC 57.246 29.630 0.00 0.00 0.00 4.06
350 378 8.818057 ACACGCACTTTCACTAATAAGATAATC 58.182 33.333 0.00 0.00 0.00 1.75
352 380 9.811995 ATACACGCACTTTCACTAATAAGATAA 57.188 29.630 0.00 0.00 0.00 1.75
354 382 8.604035 CAATACACGCACTTTCACTAATAAGAT 58.396 33.333 0.00 0.00 0.00 2.40
359 387 6.795098 TTCAATACACGCACTTTCACTAAT 57.205 33.333 0.00 0.00 0.00 1.73
360 388 6.795098 ATTCAATACACGCACTTTCACTAA 57.205 33.333 0.00 0.00 0.00 2.24
363 391 8.447787 AAATAATTCAATACACGCACTTTCAC 57.552 30.769 0.00 0.00 0.00 3.18
410 438 6.237154 GGCCAAGAGATTAGCTCAGAATAAT 58.763 40.000 0.00 0.00 46.45 1.28
423 451 2.270434 TAGGAGTGGGCCAAGAGATT 57.730 50.000 8.40 0.00 0.00 2.40
441 469 6.517362 CGGTAGCAGGAAAGATCAGAATCATA 60.517 42.308 0.00 0.00 34.07 2.15
443 471 4.442052 CGGTAGCAGGAAAGATCAGAATCA 60.442 45.833 0.00 0.00 34.07 2.57
458 486 1.392589 AATTCAATGGCCGGTAGCAG 58.607 50.000 1.90 0.00 46.50 4.24
463 491 5.675684 AGAATAAAAATTCAATGGCCGGT 57.324 34.783 1.90 0.00 33.16 5.28
466 494 6.883756 TGGGAAAGAATAAAAATTCAATGGCC 59.116 34.615 0.00 0.00 33.16 5.36
468 496 7.201548 CGCTGGGAAAGAATAAAAATTCAATGG 60.202 37.037 1.35 0.00 33.16 3.16
551 580 3.520569 AGCAACCAATGACAACAACAAC 58.479 40.909 0.00 0.00 0.00 3.32
552 581 3.883830 AGCAACCAATGACAACAACAA 57.116 38.095 0.00 0.00 0.00 2.83
553 582 3.194329 TGAAGCAACCAATGACAACAACA 59.806 39.130 0.00 0.00 0.00 3.33
582 611 5.006386 CAGCCAACCATAAGTCTTCTCTTT 58.994 41.667 0.00 0.00 0.00 2.52
608 639 7.707893 TCGTATTAATACAACTAAACTCCTGCC 59.292 37.037 22.27 0.00 32.87 4.85
632 663 4.049186 CGGACAATTTATGAGGGTAGTCG 58.951 47.826 0.00 0.00 0.00 4.18
651 682 2.682856 GCCATAAGAAATTGCAGACGGA 59.317 45.455 0.00 0.00 0.00 4.69
653 684 4.361451 AAGCCATAAGAAATTGCAGACG 57.639 40.909 0.00 0.00 0.00 4.18
702 733 1.553706 CCTTGCAGCCTTGAAGGATT 58.446 50.000 16.93 0.00 37.67 3.01
738 769 3.476552 TGAAACGCAGAAAAGAGGACAT 58.523 40.909 0.00 0.00 0.00 3.06
846 880 7.040686 GGAAACTGCTAATTCTTGGACACTAAA 60.041 37.037 0.00 0.00 0.00 1.85
862 896 4.348168 AGGAGAAGTGAAAGGAAACTGCTA 59.652 41.667 0.00 0.00 42.68 3.49
899 937 8.749026 AGAATAGGTAGTATTCAGAAACGAGA 57.251 34.615 7.35 0.00 46.81 4.04
1056 1094 0.891373 CCTCCAGCGAGAAGAGTTCA 59.109 55.000 0.00 0.00 38.52 3.18
1068 1106 1.207791 TCTCCAAATCCTCCTCCAGC 58.792 55.000 0.00 0.00 0.00 4.85
1069 1107 3.457380 TCAATCTCCAAATCCTCCTCCAG 59.543 47.826 0.00 0.00 0.00 3.86
1307 1348 8.426881 TGATTCATCATGTTAATTTGCAATGG 57.573 30.769 0.00 0.00 0.00 3.16
1319 1360 9.399797 ACTTGTGTATGTATGATTCATCATGTT 57.600 29.630 11.86 0.80 46.34 2.71
1326 1367 8.536175 TCCAGTAACTTGTGTATGTATGATTCA 58.464 33.333 0.00 0.00 0.00 2.57
1348 1389 0.549950 AGGGCATCCATGAACTCCAG 59.450 55.000 0.00 0.00 34.83 3.86
1349 1390 1.002069 AAGGGCATCCATGAACTCCA 58.998 50.000 0.00 0.00 34.83 3.86
1350 1391 1.064463 TCAAGGGCATCCATGAACTCC 60.064 52.381 0.00 0.00 37.77 3.85
1352 1393 3.053095 AGAATCAAGGGCATCCATGAACT 60.053 43.478 0.00 0.00 43.04 3.01
1373 1414 4.387862 GCTGAGGCATTTGTGAAATTTGAG 59.612 41.667 0.00 0.00 38.54 3.02
1406 1447 9.274065 CTTAGGACGCAATTGTAAATTAAGTTC 57.726 33.333 7.40 0.00 0.00 3.01
1417 1458 3.258372 TCTGTCTCTTAGGACGCAATTGT 59.742 43.478 7.40 0.00 38.91 2.71
1479 1528 9.263446 ACAGAACCACTTTTATACCTCATACTA 57.737 33.333 0.00 0.00 0.00 1.82
1484 1533 6.833041 TGAACAGAACCACTTTTATACCTCA 58.167 36.000 0.00 0.00 0.00 3.86
1485 1534 7.390718 ACATGAACAGAACCACTTTTATACCTC 59.609 37.037 0.00 0.00 0.00 3.85
1503 1552 0.824595 AGGCTGCTGCAACATGAACA 60.825 50.000 17.89 0.00 41.91 3.18
1556 1605 7.692460 TTCCGTCAAAAGATCTGTACTACTA 57.308 36.000 0.00 0.00 0.00 1.82
1599 1807 3.778629 AGTGGGGACAGTTATCCGTTATT 59.221 43.478 0.00 0.00 42.89 1.40
1836 2044 3.254060 CCCAGATCGTTGTCACAAGTAG 58.746 50.000 0.00 0.00 0.00 2.57
1838 2046 1.878102 GCCCAGATCGTTGTCACAAGT 60.878 52.381 0.00 0.00 0.00 3.16
1842 2050 1.453155 ATTGCCCAGATCGTTGTCAC 58.547 50.000 0.00 0.00 0.00 3.67
1883 2091 5.526111 GGCATCTTAACTCGGTTAGCATAAA 59.474 40.000 0.00 0.00 29.41 1.40
1884 2092 5.054477 GGCATCTTAACTCGGTTAGCATAA 58.946 41.667 0.00 0.00 29.41 1.90
1885 2093 4.502604 GGGCATCTTAACTCGGTTAGCATA 60.503 45.833 0.00 0.00 29.41 3.14
2018 2226 1.523938 GCAGACTAATGGGACGGCC 60.524 63.158 0.00 0.00 0.00 6.13
2072 2286 3.495124 TTGCTTCCAAGAAATGCGC 57.505 47.368 0.00 0.00 0.00 6.09
2097 2311 3.035363 CCCTTTGTACAGGTTTTTGGGT 58.965 45.455 0.00 0.00 30.96 4.51
2117 2331 0.111253 CCCTCATGTTGGCCTATCCC 59.889 60.000 3.32 0.00 0.00 3.85
2142 2356 1.143813 CATAACCATCCAGGAGGCCT 58.856 55.000 3.86 3.86 41.22 5.19
2143 2357 0.846693 ACATAACCATCCAGGAGGCC 59.153 55.000 0.00 0.00 41.22 5.19
2144 2358 2.736670 AACATAACCATCCAGGAGGC 57.263 50.000 0.00 0.00 41.22 4.70
2145 2359 5.310409 ACATAACATAACCATCCAGGAGG 57.690 43.478 0.00 0.00 41.22 4.30
2146 2360 6.826668 TGTACATAACATAACCATCCAGGAG 58.173 40.000 0.00 0.00 35.09 3.69
2147 2361 6.816616 TGTACATAACATAACCATCCAGGA 57.183 37.500 0.00 0.00 35.09 3.86
2157 2371 9.078753 CCGCATAACGATATGTACATAACATAA 57.921 33.333 19.11 6.39 45.90 1.90
2179 2393 3.573772 CTTCGACTCCACAGCCGCA 62.574 63.158 0.00 0.00 0.00 5.69
2180 2394 2.811317 CTTCGACTCCACAGCCGC 60.811 66.667 0.00 0.00 0.00 6.53
2261 2475 5.173854 GCAAGCAACATACAGAACTGAAAAC 59.826 40.000 8.87 0.00 0.00 2.43
2360 2575 0.179156 AAGCATACGCAGCAATGTGC 60.179 50.000 7.17 7.17 42.27 4.57
2364 2579 1.063006 CGCAAGCATACGCAGCAAT 59.937 52.632 0.00 0.00 40.31 3.56
2402 2618 4.451900 GCACAATGCAAGGTATACCTAGT 58.548 43.478 24.84 7.61 43.73 2.57
2448 2664 4.114058 AGGCATTGCATTGTAACATCAC 57.886 40.909 11.39 0.00 0.00 3.06
2449 2665 4.220163 TGAAGGCATTGCATTGTAACATCA 59.780 37.500 13.96 0.24 31.02 3.07
2450 2666 4.563976 GTGAAGGCATTGCATTGTAACATC 59.436 41.667 13.96 0.00 31.02 3.06
2452 2668 3.611293 CGTGAAGGCATTGCATTGTAACA 60.611 43.478 13.96 2.16 31.02 2.41
2477 2693 9.818270 ATAATAATTCAATCACATGGTGGAGAT 57.182 29.630 0.00 0.00 33.87 2.75
2546 2765 8.682710 GGAAGGTCAGCAACATAACAATAAATA 58.317 33.333 0.00 0.00 0.00 1.40
2547 2766 7.397192 AGGAAGGTCAGCAACATAACAATAAAT 59.603 33.333 0.00 0.00 0.00 1.40
2548 2767 6.719370 AGGAAGGTCAGCAACATAACAATAAA 59.281 34.615 0.00 0.00 0.00 1.40
2554 2773 3.944087 AGAGGAAGGTCAGCAACATAAC 58.056 45.455 0.00 0.00 0.00 1.89
2580 2799 5.410746 ACGATGATGAATATCCACATTCAGC 59.589 40.000 7.04 7.04 45.51 4.26
2599 2818 0.723414 ATGTCTGAAGCGCAACGATG 59.277 50.000 11.47 0.00 0.00 3.84
2728 2948 1.137282 GAGAGATCAAACCGAGGGACC 59.863 57.143 0.00 0.00 0.00 4.46
2767 2987 8.465999 CCTGTGATATAGGTTGACATAGATCTC 58.534 40.741 0.00 8.13 33.54 2.75
2786 3006 4.607293 TCGCTTGCTATTATCCTGTGAT 57.393 40.909 0.00 0.00 34.87 3.06
2803 3023 4.418392 GTTTCAGATGAAATGCAATCGCT 58.582 39.130 10.94 0.00 44.69 4.93
2883 3187 2.907042 ACCCCACTTCAAGAAGGTAGAG 59.093 50.000 13.83 2.19 42.53 2.43
2892 3196 2.489329 CACAGCATTACCCCACTTCAAG 59.511 50.000 0.00 0.00 0.00 3.02
2942 3246 3.724478 ACTCCTCCATGTGGATCTTGTA 58.276 45.455 1.54 0.00 44.46 2.41
2960 3265 8.019656 TGAGGATTGTTCCCTTTAGTATACTC 57.980 38.462 9.12 0.00 43.76 2.59


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

AutoCloner maintained by Alex Coulton.