Multiple sequence alignment - TraesCS1D01G114700

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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 TraesCS1D01G114700 chr1D 100.000 4542 0 0 1 4542 110658588 110663129 0.000000e+00 8388.0
1 TraesCS1D01G114700 chr1D 90.862 1346 96 12 2488 3813 110604891 110606229 0.000000e+00 1779.0
2 TraesCS1D01G114700 chr1D 90.337 445 27 9 1090 1528 110603422 110603856 1.830000e-158 569.0
3 TraesCS1D01G114700 chr1D 83.953 592 65 9 1692 2282 110604232 110604794 1.440000e-149 540.0
4 TraesCS1D01G114700 chr1D 86.842 152 16 2 4394 4541 110690998 110691149 2.810000e-37 167.0
5 TraesCS1D01G114700 chr1D 78.543 247 12 19 627 845 110602979 110603212 1.720000e-24 124.0
6 TraesCS1D01G114700 chr1B 91.741 3378 136 53 578 3852 168621245 168624582 0.000000e+00 4560.0
7 TraesCS1D01G114700 chr1B 90.229 1351 88 23 2488 3813 168417741 168419072 0.000000e+00 1724.0
8 TraesCS1D01G114700 chr1B 93.233 665 38 5 3882 4541 168624912 168625574 0.000000e+00 972.0
9 TraesCS1D01G114700 chr1B 90.787 445 31 8 1090 1528 168416263 168416703 1.820000e-163 586.0
10 TraesCS1D01G114700 chr1B 84.471 586 63 7 1692 2276 168417080 168417638 1.850000e-153 553.0
11 TraesCS1D01G114700 chr1B 87.931 116 8 3 731 845 168415918 168416028 1.030000e-26 132.0
12 TraesCS1D01G114700 chr1A 93.588 2776 124 26 1090 3834 115975982 115978734 0.000000e+00 4091.0
13 TraesCS1D01G114700 chr1A 90.639 1346 99 13 2488 3813 115971113 115972451 0.000000e+00 1762.0
14 TraesCS1D01G114700 chr1A 92.571 525 11 14 578 1075 115975418 115975941 0.000000e+00 728.0
15 TraesCS1D01G114700 chr1A 91.304 506 44 0 3886 4391 115978879 115979384 0.000000e+00 691.0
16 TraesCS1D01G114700 chr1A 88.989 445 37 9 1090 1528 115949698 115950136 1.440000e-149 540.0
17 TraesCS1D01G114700 chr1A 83.333 600 65 11 1692 2288 115970457 115971024 5.210000e-144 521.0
18 TraesCS1D01G114700 chr1A 79.825 228 29 12 627 845 115949199 115949418 2.830000e-32 150.0
19 TraesCS1D01G114700 chr1A 90.323 93 7 2 2405 2495 249435294 249435202 2.220000e-23 121.0
20 TraesCS1D01G114700 chr5D 95.763 590 23 2 1 588 432505911 432505322 0.000000e+00 950.0
21 TraesCS1D01G114700 chr7D 96.062 584 20 3 1 581 550271717 550271134 0.000000e+00 948.0
22 TraesCS1D01G114700 chr7D 96.200 579 18 3 1 578 555373573 555372998 0.000000e+00 944.0
23 TraesCS1D01G114700 chr7D 95.869 581 22 2 1 579 460639585 460640165 0.000000e+00 939.0
24 TraesCS1D01G114700 chr7D 95.377 584 23 4 1 581 160666283 160666865 0.000000e+00 926.0
25 TraesCS1D01G114700 chr7D 95.377 584 23 4 1 581 160690742 160691324 0.000000e+00 926.0
26 TraesCS1D01G114700 chr6D 96.034 580 20 3 1 578 413389314 413388736 0.000000e+00 941.0
27 TraesCS1D01G114700 chr6D 90.833 120 8 1 1529 1645 384220927 384221046 1.690000e-34 158.0
28 TraesCS1D01G114700 chr6D 92.222 90 6 1 2398 2487 122992103 122992191 4.770000e-25 126.0
29 TraesCS1D01G114700 chr3D 95.883 583 20 4 1 579 578844067 578843485 0.000000e+00 941.0
30 TraesCS1D01G114700 chr3D 90.833 120 6 3 1528 1644 537915013 537914896 6.080000e-34 156.0
31 TraesCS1D01G114700 chr3D 89.344 122 9 2 1529 1646 107672217 107672338 2.830000e-32 150.0
32 TraesCS1D01G114700 chr2D 95.855 579 21 2 1 578 556180903 556180327 0.000000e+00 933.0
33 TraesCS1D01G114700 chr2D 90.833 120 8 1 1529 1645 607675859 607675740 1.690000e-34 158.0
34 TraesCS1D01G114700 chr2D 77.692 130 27 2 3897 4025 21186980 21187108 1.350000e-10 78.7
35 TraesCS1D01G114700 chr4A 82.573 241 40 1 2779 3017 547298075 547297835 1.280000e-50 211.0
36 TraesCS1D01G114700 chr4B 88.742 151 11 5 4395 4541 87018757 87018609 3.610000e-41 180.0
37 TraesCS1D01G114700 chr4B 89.916 119 7 3 1529 1643 167349965 167350082 1.020000e-31 148.0
38 TraesCS1D01G114700 chr7B 90.833 120 8 1 1529 1645 511462211 511462092 1.690000e-34 158.0
39 TraesCS1D01G114700 chr7B 92.135 89 6 1 2406 2493 533304509 533304597 1.720000e-24 124.0
40 TraesCS1D01G114700 chr7B 91.111 90 7 1 2398 2487 552011764 552011852 2.220000e-23 121.0
41 TraesCS1D01G114700 chr2B 90.833 120 8 1 1529 1645 296067484 296067365 1.690000e-34 158.0
42 TraesCS1D01G114700 chr2B 91.011 89 8 0 2399 2487 394722948 394723036 2.220000e-23 121.0
43 TraesCS1D01G114700 chrUn 84.615 156 17 7 4391 4541 293730458 293730611 1.020000e-31 148.0
44 TraesCS1D01G114700 chrUn 84.615 156 17 7 4391 4541 469618203 469618050 1.020000e-31 148.0
45 TraesCS1D01G114700 chr7A 84.314 153 18 5 4393 4541 127873928 127874078 1.320000e-30 145.0
46 TraesCS1D01G114700 chr5A 88.983 118 9 2 1529 1643 227926412 227926528 4.740000e-30 143.0
47 TraesCS1D01G114700 chr6A 93.478 92 6 0 2400 2491 548408147 548408056 2.200000e-28 137.0
48 TraesCS1D01G114700 chr2A 91.209 91 7 1 2397 2487 385002793 385002704 6.170000e-24 122.0


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 TraesCS1D01G114700 chr1D 110658588 110663129 4541 False 8388.00 8388 100.00000 1 4542 1 chr1D.!!$F1 4541
1 TraesCS1D01G114700 chr1D 110602979 110606229 3250 False 753.00 1779 85.92375 627 3813 4 chr1D.!!$F3 3186
2 TraesCS1D01G114700 chr1B 168621245 168625574 4329 False 2766.00 4560 92.48700 578 4541 2 chr1B.!!$F2 3963
3 TraesCS1D01G114700 chr1B 168415918 168419072 3154 False 748.75 1724 88.35450 731 3813 4 chr1B.!!$F1 3082
4 TraesCS1D01G114700 chr1A 115970457 115979384 8927 False 1558.60 4091 90.28700 578 4391 5 chr1A.!!$F2 3813
5 TraesCS1D01G114700 chr1A 115949199 115950136 937 False 345.00 540 84.40700 627 1528 2 chr1A.!!$F1 901
6 TraesCS1D01G114700 chr5D 432505322 432505911 589 True 950.00 950 95.76300 1 588 1 chr5D.!!$R1 587
7 TraesCS1D01G114700 chr7D 550271134 550271717 583 True 948.00 948 96.06200 1 581 1 chr7D.!!$R1 580
8 TraesCS1D01G114700 chr7D 555372998 555373573 575 True 944.00 944 96.20000 1 578 1 chr7D.!!$R2 577
9 TraesCS1D01G114700 chr7D 460639585 460640165 580 False 939.00 939 95.86900 1 579 1 chr7D.!!$F3 578
10 TraesCS1D01G114700 chr7D 160666283 160666865 582 False 926.00 926 95.37700 1 581 1 chr7D.!!$F1 580
11 TraesCS1D01G114700 chr7D 160690742 160691324 582 False 926.00 926 95.37700 1 581 1 chr7D.!!$F2 580
12 TraesCS1D01G114700 chr6D 413388736 413389314 578 True 941.00 941 96.03400 1 578 1 chr6D.!!$R1 577
13 TraesCS1D01G114700 chr3D 578843485 578844067 582 True 941.00 941 95.88300 1 579 1 chr3D.!!$R2 578
14 TraesCS1D01G114700 chr2D 556180327 556180903 576 True 933.00 933 95.85500 1 578 1 chr2D.!!$R1 577

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
669 5055 0.107410 AGCAAACTTGTCGACACCCA 60.107 50.000 19.90 2.47 0.00 4.51 F
800 5212 0.108472 GCAGAAAGAAATGCAGGGGC 60.108 55.000 0.00 0.00 42.11 5.80 F
1406 5947 0.944386 CCAATGGCGAAATACCCGAG 59.056 55.000 0.00 0.00 0.00 4.63 F
1552 6097 1.067212 CCCTCTGTCCGGAATTACTCG 59.933 57.143 5.23 0.00 0.00 4.18 F
1897 6775 1.257743 TATGGCAGAGGGCTATCGAC 58.742 55.000 0.00 0.00 43.38 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 6553 0.390209 GTTGGGCATGTGGAATGTGC 60.390 55.000 0.00 0.0 38.12 4.57 R
2005 6883 1.004560 CTTCCTGCCAGCGAACTCA 60.005 57.895 0.00 0.0 0.00 3.41 R
3203 8109 0.679640 CGGTTGCAGGGCCTAAATGA 60.680 55.000 5.28 0.0 0.00 2.57 R
3445 8368 1.508632 CGGTGAAATCGGTGAACAGT 58.491 50.000 0.00 0.0 0.00 3.55 R
3686 8611 0.321653 AGTTGCCACTTCCCGTGATC 60.322 55.000 0.00 0.0 46.81 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
428 432 1.286553 GAGAGTGAGGAAGAGGGAGGA 59.713 57.143 0.00 0.00 0.00 3.71
435 439 0.692756 GGAAGAGGGAGGAAGAGGGG 60.693 65.000 0.00 0.00 0.00 4.79
443 447 0.836400 GAGGAAGAGGGGGTGTGTGA 60.836 60.000 0.00 0.00 0.00 3.58
491 497 8.072238 TCGTCAATGTCACTTAATATGTATGC 57.928 34.615 0.00 0.00 0.00 3.14
549 555 9.791801 ATTGAACTTTTAAATTTAATGTGGCCT 57.208 25.926 11.33 0.38 0.00 5.19
669 5055 0.107410 AGCAAACTTGTCGACACCCA 60.107 50.000 19.90 2.47 0.00 4.51
729 5116 2.288642 ATAGGTACGGGACAGCCGGA 62.289 60.000 5.05 0.00 37.87 5.14
800 5212 0.108472 GCAGAAAGAAATGCAGGGGC 60.108 55.000 0.00 0.00 42.11 5.80
933 5346 2.446435 AGCTTCTCTGACTCTGACTCC 58.554 52.381 0.00 0.00 0.00 3.85
1194 5730 5.661056 TGGTTCGTCAGAATCTTCAGTAT 57.339 39.130 0.00 0.00 38.30 2.12
1215 5756 9.383519 CAGTATTTGCTTAGTTTCAAGATCCTA 57.616 33.333 0.00 0.00 0.00 2.94
1357 5898 2.304180 AGAAGCAGCCACTACAGACATT 59.696 45.455 0.00 0.00 0.00 2.71
1406 5947 0.944386 CCAATGGCGAAATACCCGAG 59.056 55.000 0.00 0.00 0.00 4.63
1481 6023 3.314635 CCTTCCTTCTATGTTGCATCAGC 59.685 47.826 3.50 0.00 42.57 4.26
1496 6038 4.202192 TGCATCAGCTTCAGATGGTAGTAG 60.202 45.833 12.88 0.00 42.38 2.57
1501 6043 7.747155 TCAGCTTCAGATGGTAGTAGTATAC 57.253 40.000 0.00 0.00 35.26 1.47
1528 6070 2.425312 TGCCACGTCAAATTCAACTGTT 59.575 40.909 0.00 0.00 0.00 3.16
1529 6071 3.628032 TGCCACGTCAAATTCAACTGTTA 59.372 39.130 0.00 0.00 0.00 2.41
1530 6072 3.972502 GCCACGTCAAATTCAACTGTTAC 59.027 43.478 0.00 0.00 0.00 2.50
1534 6076 4.514066 ACGTCAAATTCAACTGTTACTCCC 59.486 41.667 0.00 0.00 0.00 4.30
1535 6077 4.755123 CGTCAAATTCAACTGTTACTCCCT 59.245 41.667 0.00 0.00 0.00 4.20
1537 6079 5.998363 GTCAAATTCAACTGTTACTCCCTCT 59.002 40.000 0.00 0.00 0.00 3.69
1538 6080 5.997746 TCAAATTCAACTGTTACTCCCTCTG 59.002 40.000 0.00 0.00 0.00 3.35
1540 6082 4.602340 TTCAACTGTTACTCCCTCTGTC 57.398 45.455 0.00 0.00 0.00 3.51
1542 6084 1.546961 ACTGTTACTCCCTCTGTCCG 58.453 55.000 0.00 0.00 0.00 4.79
1552 6097 1.067212 CCCTCTGTCCGGAATTACTCG 59.933 57.143 5.23 0.00 0.00 4.18
1568 6113 9.378551 GGAATTACTCGCATAAATGGATGTATA 57.621 33.333 0.00 0.00 0.00 1.47
1574 6119 7.915923 ACTCGCATAAATGGATGTATATAGACG 59.084 37.037 0.00 0.00 0.00 4.18
1577 6122 9.678941 CGCATAAATGGATGTATATAGACGTAT 57.321 33.333 0.00 0.00 0.00 3.06
1608 6153 9.607333 AGTTCTAGATACATCCATTTCTATCCA 57.393 33.333 0.00 0.00 0.00 3.41
1628 6173 6.961359 TCCATTTCTGTGACAAGTAATACG 57.039 37.500 0.00 0.00 0.00 3.06
1630 6175 5.872617 CCATTTCTGTGACAAGTAATACGGA 59.127 40.000 0.00 0.00 0.00 4.69
1632 6177 7.065803 CCATTTCTGTGACAAGTAATACGGAAT 59.934 37.037 0.00 0.00 38.00 3.01
1646 6191 1.768870 ACGGAATGGAGGGAGTATTGG 59.231 52.381 0.00 0.00 0.00 3.16
1654 6199 3.714798 TGGAGGGAGTATTGGGTATTGAC 59.285 47.826 0.00 0.00 0.00 3.18
1692 6553 8.530311 TCAGTACCCGAGAAGACTATAGTATAG 58.470 40.741 14.53 14.53 0.00 1.31
1693 6554 7.278424 CAGTACCCGAGAAGACTATAGTATAGC 59.722 44.444 15.80 9.51 0.00 2.97
1694 6555 6.124316 ACCCGAGAAGACTATAGTATAGCA 57.876 41.667 15.80 0.00 0.00 3.49
1695 6556 5.939296 ACCCGAGAAGACTATAGTATAGCAC 59.061 44.000 15.80 10.78 0.00 4.40
1696 6557 5.938710 CCCGAGAAGACTATAGTATAGCACA 59.061 44.000 15.80 0.00 0.00 4.57
1697 6558 6.600032 CCCGAGAAGACTATAGTATAGCACAT 59.400 42.308 15.80 5.10 0.00 3.21
1698 6559 7.121463 CCCGAGAAGACTATAGTATAGCACATT 59.879 40.741 15.80 6.74 0.00 2.71
1699 6560 8.178964 CCGAGAAGACTATAGTATAGCACATTC 58.821 40.741 15.80 13.61 0.00 2.67
1712 6583 1.259609 CACATTCCACATGCCCAACT 58.740 50.000 0.00 0.00 0.00 3.16
1725 6596 3.620488 TGCCCAACTATGATGAAAGGAC 58.380 45.455 0.00 0.00 0.00 3.85
1776 6648 4.284829 TGTCATGTCCAGATTGTTAGCA 57.715 40.909 0.00 0.00 0.00 3.49
1873 6751 5.650266 ACCGAACCTGAATATATTTGTGCAA 59.350 36.000 0.00 0.00 0.00 4.08
1897 6775 1.257743 TATGGCAGAGGGCTATCGAC 58.742 55.000 0.00 0.00 43.38 4.20
1915 6793 2.417719 GACGAAGGTGCAGACTTCATT 58.582 47.619 23.36 13.71 43.43 2.57
1984 6862 6.706295 TCATGATGTAACACTGGATAACACA 58.294 36.000 0.00 0.00 0.00 3.72
2005 6883 2.494918 GACATCGCCAGCCGTACT 59.505 61.111 0.00 0.00 38.35 2.73
2164 7043 7.565680 TCTACTTCTGACTTTTGGAGTTCTTT 58.434 34.615 0.00 0.00 39.19 2.52
2427 7310 5.888982 ACCTCCGATCCATAATAAGTGTT 57.111 39.130 0.00 0.00 0.00 3.32
2431 7314 5.432645 TCCGATCCATAATAAGTGTTGCAA 58.567 37.500 0.00 0.00 0.00 4.08
2540 7436 8.256611 TCTTGTTTCTTTGCTACTGCTAATAG 57.743 34.615 0.00 0.00 40.48 1.73
2720 7617 7.012989 ACTCCTGGAACACATTGTTTACTTAAC 59.987 37.037 0.00 0.00 41.28 2.01
2891 7796 9.011095 CAAATATATGTCTGAAGATTGGCTCAT 57.989 33.333 0.00 0.00 0.00 2.90
3113 8019 7.418337 TTCTAACCTGCAGTCATACTATGAA 57.582 36.000 13.81 2.07 41.69 2.57
3275 8198 6.108687 TCTTCAGGTGAGCAAGTTATACATG 58.891 40.000 0.00 0.00 0.00 3.21
3297 8220 6.926630 TGTACATATACATATGCCAGGTCA 57.073 37.500 1.58 0.00 42.98 4.02
3483 8406 2.633860 GCAGCTTGCACAAGTACCT 58.366 52.632 11.77 0.00 44.26 3.08
3581 8504 6.039717 TGAAGTTTGATGCTCACTAAAGCTTT 59.960 34.615 17.30 17.30 42.94 3.51
3686 8611 7.224753 ACCATTCTATGTAATTGCTTCGTACAG 59.775 37.037 0.00 0.00 31.61 2.74
3882 8951 4.873129 CGCGACCGGTCATCTGGG 62.873 72.222 32.80 20.43 44.02 4.45
3893 9120 2.435805 GGTCATCTGGGCTGTAGAATCA 59.564 50.000 0.00 0.00 0.00 2.57
3899 9126 6.319658 TCATCTGGGCTGTAGAATCATTTTTC 59.680 38.462 0.00 0.00 0.00 2.29
3905 9132 8.271458 TGGGCTGTAGAATCATTTTTCATACTA 58.729 33.333 0.00 0.00 0.00 1.82
3950 9177 4.538738 AGACCTCCTAACTCTGATACCAC 58.461 47.826 0.00 0.00 0.00 4.16
3968 9195 7.774625 TGATACCACATTGAATTCATGCTCTAA 59.225 33.333 9.40 0.00 0.00 2.10
3973 9200 7.262772 CACATTGAATTCATGCTCTAACCAAT 58.737 34.615 9.40 0.00 0.00 3.16
3977 9204 7.465353 TGAATTCATGCTCTAACCAATTCAA 57.535 32.000 3.38 0.00 37.32 2.69
3978 9205 8.070034 TGAATTCATGCTCTAACCAATTCAAT 57.930 30.769 3.38 0.00 37.32 2.57
3984 9211 8.366401 TCATGCTCTAACCAATTCAATCAAAAA 58.634 29.630 0.00 0.00 0.00 1.94
3986 9213 9.729281 ATGCTCTAACCAATTCAATCAAAAATT 57.271 25.926 0.00 0.00 0.00 1.82
4098 9325 4.301628 GGCTGACATTTAATTATGCCTGC 58.698 43.478 0.00 0.00 36.52 4.85
4130 9357 7.669427 TCTTTTTGTCGGTATGGTCTTACTTA 58.331 34.615 0.00 0.00 0.00 2.24
4450 9679 4.162690 GACCCTTGATCCGCGCCT 62.163 66.667 0.00 0.00 0.00 5.52
4456 9685 1.825285 CTTGATCCGCGCCTTGATCG 61.825 60.000 18.61 7.04 40.19 3.69
4485 9714 0.322187 AACCCACCTATGGTTGACGC 60.322 55.000 0.00 0.00 45.66 5.19
4486 9715 1.451387 CCCACCTATGGTTGACGCC 60.451 63.158 0.00 0.00 45.66 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
234 237 3.366985 CCAAAAGGACGATGTAAAAGGGC 60.367 47.826 0.00 0.00 0.00 5.19
340 344 3.088789 ACGGAGACTACCAACTGAGAT 57.911 47.619 0.00 0.00 0.00 2.75
428 432 0.191064 TCTCTCACACACCCCCTCTT 59.809 55.000 0.00 0.00 0.00 2.85
435 439 4.074970 ACCATCAAATTCTCTCACACACC 58.925 43.478 0.00 0.00 0.00 4.16
465 471 8.712363 GCATACATATTAAGTGACATTGACGAT 58.288 33.333 0.00 0.00 0.00 3.73
729 5116 2.108168 TCGATTGGAGTCGGAATTCCT 58.892 47.619 22.05 3.47 41.74 3.36
933 5346 2.578714 GCCTCCTCCTCCGCCTATG 61.579 68.421 0.00 0.00 0.00 2.23
1035 5459 6.128486 TGCATTATTCAGAGAGAGAGAGAGT 58.872 40.000 0.00 0.00 0.00 3.24
1215 5756 6.318144 CCTGTCAGAGAATGCATTCAGTTTAT 59.682 38.462 34.59 17.53 39.23 1.40
1314 5855 2.371841 TGTGGTTTACATCCAGCTGACT 59.628 45.455 17.39 0.00 35.49 3.41
1357 5898 1.544724 GGCAATGTTGTAAGGCCTGA 58.455 50.000 5.69 0.00 41.39 3.86
1406 5947 0.533755 AATATGCCGCAGCTGTCTCC 60.534 55.000 16.64 2.31 40.80 3.71
1496 6038 6.657836 ATTTGACGTGGCACTAAAGTATAC 57.342 37.500 16.72 0.00 0.00 1.47
1501 6043 4.481930 TGAATTTGACGTGGCACTAAAG 57.518 40.909 16.72 2.12 0.00 1.85
1509 6051 5.418310 AGTAACAGTTGAATTTGACGTGG 57.582 39.130 0.00 0.00 0.00 4.94
1528 6070 2.544844 AATTCCGGACAGAGGGAGTA 57.455 50.000 1.83 0.00 33.01 2.59
1529 6071 2.108970 GTAATTCCGGACAGAGGGAGT 58.891 52.381 1.83 0.00 33.01 3.85
1530 6072 2.362717 GAGTAATTCCGGACAGAGGGAG 59.637 54.545 1.83 0.00 33.01 4.30
1534 6076 1.134367 TGCGAGTAATTCCGGACAGAG 59.866 52.381 1.83 0.00 0.00 3.35
1535 6077 1.179152 TGCGAGTAATTCCGGACAGA 58.821 50.000 1.83 0.00 0.00 3.41
1537 6079 3.804786 TTATGCGAGTAATTCCGGACA 57.195 42.857 1.83 0.00 0.00 4.02
1538 6080 4.084013 CCATTTATGCGAGTAATTCCGGAC 60.084 45.833 1.83 0.00 0.00 4.79
1540 6082 4.062293 TCCATTTATGCGAGTAATTCCGG 58.938 43.478 0.00 0.00 0.00 5.14
1542 6084 6.560253 ACATCCATTTATGCGAGTAATTCC 57.440 37.500 0.00 0.00 0.00 3.01
1589 6134 9.512588 ACAGAAATGGATAGAAATGGATGTATC 57.487 33.333 0.00 0.00 0.00 2.24
1602 6147 8.755941 CGTATTACTTGTCACAGAAATGGATAG 58.244 37.037 0.00 0.00 0.00 2.08
1603 6148 7.709182 CCGTATTACTTGTCACAGAAATGGATA 59.291 37.037 0.00 0.00 0.00 2.59
1604 6149 6.538742 CCGTATTACTTGTCACAGAAATGGAT 59.461 38.462 0.00 0.00 0.00 3.41
1605 6150 5.872617 CCGTATTACTTGTCACAGAAATGGA 59.127 40.000 0.00 0.00 0.00 3.41
1606 6151 5.872617 TCCGTATTACTTGTCACAGAAATGG 59.127 40.000 0.00 0.00 0.00 3.16
1607 6152 6.961359 TCCGTATTACTTGTCACAGAAATG 57.039 37.500 0.00 0.00 0.00 2.32
1608 6153 7.065803 CCATTCCGTATTACTTGTCACAGAAAT 59.934 37.037 0.00 0.00 0.00 2.17
1609 6154 6.370442 CCATTCCGTATTACTTGTCACAGAAA 59.630 38.462 0.00 0.00 0.00 2.52
1610 6155 5.872617 CCATTCCGTATTACTTGTCACAGAA 59.127 40.000 0.00 0.00 0.00 3.02
1611 6156 5.186215 TCCATTCCGTATTACTTGTCACAGA 59.814 40.000 0.00 0.00 0.00 3.41
1612 6157 5.416083 TCCATTCCGTATTACTTGTCACAG 58.584 41.667 0.00 0.00 0.00 3.66
1626 6171 1.768870 CCAATACTCCCTCCATTCCGT 59.231 52.381 0.00 0.00 0.00 4.69
1628 6173 2.136026 ACCCAATACTCCCTCCATTCC 58.864 52.381 0.00 0.00 0.00 3.01
1630 6175 4.981647 TCAATACCCAATACTCCCTCCATT 59.018 41.667 0.00 0.00 0.00 3.16
1632 6177 3.714798 GTCAATACCCAATACTCCCTCCA 59.285 47.826 0.00 0.00 0.00 3.86
1646 6191 7.362802 ACTGAAGACTATTAGGGTCAATACC 57.637 40.000 0.00 0.00 45.97 2.73
1654 6199 4.467769 TCGGGTACTGAAGACTATTAGGG 58.532 47.826 0.00 0.00 43.00 3.53
1692 6553 0.390209 GTTGGGCATGTGGAATGTGC 60.390 55.000 0.00 0.00 38.12 4.57
1693 6554 1.259609 AGTTGGGCATGTGGAATGTG 58.740 50.000 0.00 0.00 0.00 3.21
1694 6555 2.897271 TAGTTGGGCATGTGGAATGT 57.103 45.000 0.00 0.00 0.00 2.71
1695 6556 3.289836 TCATAGTTGGGCATGTGGAATG 58.710 45.455 0.00 0.00 0.00 2.67
1696 6557 3.668141 TCATAGTTGGGCATGTGGAAT 57.332 42.857 0.00 0.00 0.00 3.01
1697 6558 3.053768 TCATCATAGTTGGGCATGTGGAA 60.054 43.478 0.00 0.00 0.00 3.53
1698 6559 2.509131 TCATCATAGTTGGGCATGTGGA 59.491 45.455 0.00 0.00 0.00 4.02
1699 6560 2.934887 TCATCATAGTTGGGCATGTGG 58.065 47.619 0.00 0.00 0.00 4.17
1712 6583 5.049828 CAGCATACACGTCCTTTCATCATA 58.950 41.667 0.00 0.00 0.00 2.15
1725 6596 3.675225 CGGGATATTCTTCAGCATACACG 59.325 47.826 0.00 0.00 0.00 4.49
1846 6718 7.033185 GCACAAATATATTCAGGTTCGGTTTT 58.967 34.615 0.00 0.00 0.00 2.43
1873 6751 3.557898 CGATAGCCCTCTGCCATAAACAT 60.558 47.826 0.00 0.00 42.71 2.71
1897 6775 2.414481 CTCAATGAAGTCTGCACCTTCG 59.586 50.000 13.80 3.82 40.96 3.79
1915 6793 6.015603 CCTCTGATGCAAGTATATCAGTCTCA 60.016 42.308 11.45 0.00 46.50 3.27
2005 6883 1.004560 CTTCCTGCCAGCGAACTCA 60.005 57.895 0.00 0.00 0.00 3.41
2164 7043 5.701224 AGTGTAAAATCCACTGGAGGAAAA 58.299 37.500 3.62 0.00 41.47 2.29
2167 7046 5.783360 TCTTAGTGTAAAATCCACTGGAGGA 59.217 40.000 3.62 0.00 42.85 3.71
2169 7048 6.936279 TCTCTTAGTGTAAAATCCACTGGAG 58.064 40.000 3.62 13.85 42.85 3.86
2296 7176 7.770897 AGAGTCATATTTAAGGGCAGTAAACTG 59.229 37.037 5.73 5.73 46.40 3.16
2297 7177 7.862675 AGAGTCATATTTAAGGGCAGTAAACT 58.137 34.615 0.00 0.00 0.00 2.66
2298 7178 7.769044 TGAGAGTCATATTTAAGGGCAGTAAAC 59.231 37.037 0.00 0.00 0.00 2.01
2365 7247 2.158957 AGGCATCCGAATTACACACGAT 60.159 45.455 0.00 0.00 0.00 3.73
2427 7310 3.964031 ACTGGGGTTAGTTCAAAATTGCA 59.036 39.130 0.00 0.00 0.00 4.08
2540 7436 5.304614 TCCCTGCAATATAGTAGGAGAACAC 59.695 44.000 0.00 0.00 43.25 3.32
2720 7617 9.398170 CAGTAGACATTAAAGTTGGTTCATTTG 57.602 33.333 0.00 0.00 0.00 2.32
2891 7796 2.708216 TTGGATGAATAGCGGCTTCA 57.292 45.000 8.26 7.40 37.06 3.02
3045 7950 2.754946 TCGGGTGATGAACTTGGTAC 57.245 50.000 0.00 0.00 0.00 3.34
3113 8019 4.288531 CGAGATAGCCGTTCGAAGTTATT 58.711 43.478 0.00 0.00 36.49 1.40
3203 8109 0.679640 CGGTTGCAGGGCCTAAATGA 60.680 55.000 5.28 0.00 0.00 2.57
3275 8198 8.914011 TCTATGACCTGGCATATGTATATGTAC 58.086 37.037 12.14 7.42 41.63 2.90
3297 8220 5.939764 TCAGCAAGGTACTGTTCATCTAT 57.060 39.130 0.00 0.00 40.86 1.98
3445 8368 1.508632 CGGTGAAATCGGTGAACAGT 58.491 50.000 0.00 0.00 0.00 3.55
3581 8504 2.910319 AGGTATACAGACTTGGCAACCA 59.090 45.455 5.01 0.00 0.00 3.67
3616 8541 4.201881 GGTACCGACAACAATGAAATAGCC 60.202 45.833 0.00 0.00 0.00 3.93
3681 8606 1.739371 GCCACTTCCCGTGATCTGTAC 60.739 57.143 0.00 0.00 46.81 2.90
3686 8611 0.321653 AGTTGCCACTTCCCGTGATC 60.322 55.000 0.00 0.00 46.81 2.92
3781 8706 8.177013 GCATGCCAAATTATCCAGTTTTAAAAG 58.823 33.333 6.36 0.00 0.00 2.27
3852 8777 1.226888 GTCGCGGCTAGGGTTACTG 60.227 63.158 1.90 0.00 0.00 2.74
3880 8949 7.573968 AGTATGAAAAATGATTCTACAGCCC 57.426 36.000 0.00 0.00 0.00 5.19
3899 9126 9.770097 AGTTCAAGACCATATCAACATAGTATG 57.230 33.333 8.66 8.66 0.00 2.39
3937 9164 7.415989 GCATGAATTCAATGTGGTATCAGAGTT 60.416 37.037 13.09 0.00 0.00 3.01
3950 9177 7.977293 TGAATTGGTTAGAGCATGAATTCAATG 59.023 33.333 13.09 12.00 31.45 2.82
3968 9195 9.881529 CAAATTCGAATTTTTGATTGAATTGGT 57.118 25.926 28.91 4.32 36.52 3.67
3978 9205 9.677567 CCTCTCTTTACAAATTCGAATTTTTGA 57.322 29.630 28.91 18.96 36.52 2.69
3984 9211 4.332819 CCGCCTCTCTTTACAAATTCGAAT 59.667 41.667 4.39 4.39 0.00 3.34
3986 9213 3.259064 CCGCCTCTCTTTACAAATTCGA 58.741 45.455 0.00 0.00 0.00 3.71
3991 9218 0.398696 TGCCCGCCTCTCTTTACAAA 59.601 50.000 0.00 0.00 0.00 2.83
3993 9220 0.618458 ATTGCCCGCCTCTCTTTACA 59.382 50.000 0.00 0.00 0.00 2.41
3997 9224 4.373156 AAATATATTGCCCGCCTCTCTT 57.627 40.909 0.00 0.00 0.00 2.85
4035 9262 1.286260 GAGCCGTCGTCTGACAACT 59.714 57.895 8.73 0.00 45.80 3.16
4098 9325 5.178067 ACCATACCGACAAAAAGAACTAACG 59.822 40.000 0.00 0.00 0.00 3.18
4130 9357 1.417890 CAACAACTCTCTCCACCCACT 59.582 52.381 0.00 0.00 0.00 4.00
4368 9595 1.864711 AGTTGACAATGACACGAACCG 59.135 47.619 0.00 0.00 0.00 4.44
4433 9662 3.682292 AAGGCGCGGATCAAGGGTC 62.682 63.158 8.83 0.00 0.00 4.46
4492 9721 2.230750 ACCTCTTTATATAGCCCGCGAC 59.769 50.000 8.23 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.