Multiple sequence alignment - TraesCS2A01G524800

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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 TraesCS2A01G524800 chr2A 100.000 2819 0 0 1 2819 745406876 745409694 0.000000e+00 5206.0
1 TraesCS2A01G524800 chr2D 86.082 1516 98 46 1282 2735 615400838 615402302 0.000000e+00 1526.0
2 TraesCS2A01G524800 chr2D 84.802 658 50 19 660 1310 615400225 615400839 1.430000e-172 616.0
3 TraesCS2A01G524800 chr2D 85.097 463 18 14 228 659 615399425 615399867 2.600000e-115 425.0
4 TraesCS2A01G524800 chr2D 95.429 175 8 0 51 225 615398705 615398879 2.140000e-71 279.0
5 TraesCS2A01G524800 chr2B 85.797 1204 79 35 1246 2413 749854245 749855392 0.000000e+00 1192.0
6 TraesCS2A01G524800 chr2B 87.671 730 37 24 651 1352 749853587 749854291 0.000000e+00 800.0
7 TraesCS2A01G524800 chr2B 84.061 458 23 12 228 659 749851583 749852016 2.040000e-106 396.0
8 TraesCS2A01G524800 chr2B 84.461 399 34 16 2436 2819 749855456 749855841 4.440000e-98 368.0
9 TraesCS2A01G524800 chr2B 94.175 103 6 0 51 153 749850651 749850753 1.050000e-34 158.0
10 TraesCS2A01G524800 chr2B 87.692 65 7 1 407 471 749850631 749850694 1.080000e-09 75.0
11 TraesCS2A01G524800 chr7B 100.000 52 0 0 2 53 1283776 1283827 2.310000e-16 97.1
12 TraesCS2A01G524800 chr7B 98.077 52 1 0 2 53 28960742 28960793 1.080000e-14 91.6
13 TraesCS2A01G524800 chr3A 100.000 52 0 0 2 53 551729027 551729078 2.310000e-16 97.1
14 TraesCS2A01G524800 chr5A 100.000 51 0 0 2 52 687871734 687871684 8.310000e-16 95.3
15 TraesCS2A01G524800 chr1D 100.000 51 0 0 2 52 464031249 464031199 8.310000e-16 95.3
16 TraesCS2A01G524800 chr6B 98.077 52 1 0 2 53 632889483 632889534 1.080000e-14 91.6
17 TraesCS2A01G524800 chr6D 93.548 62 1 3 6 67 34581529 34581587 3.870000e-14 89.8
18 TraesCS2A01G524800 chr1B 98.039 51 1 0 2 52 190318867 190318917 3.870000e-14 89.8
19 TraesCS2A01G524800 chr3D 92.857 56 4 0 2 57 569803749 569803804 6.470000e-12 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 TraesCS2A01G524800 chr2A 745406876 745409694 2818 False 5206.000000 5206 100.0000 1 2819 1 chr2A.!!$F1 2818
1 TraesCS2A01G524800 chr2D 615398705 615402302 3597 False 711.500000 1526 87.8525 51 2735 4 chr2D.!!$F1 2684
2 TraesCS2A01G524800 chr2B 749850631 749855841 5210 False 498.166667 1192 87.3095 51 2819 6 chr2B.!!$F1 2768

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
313 1150 0.107508 CACTCGGCAGGGATGAACAT 60.108 55.0 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 4873 0.169672 AATACGAGACCACCGACACG 59.83 55.0 0.0 0.0 0.0 4.49 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
47 48 8.658499 ACGCTTTTATATTAGTTTACAGAGGG 57.342 34.615 0.00 0.00 0.00 4.30
48 49 8.480501 ACGCTTTTATATTAGTTTACAGAGGGA 58.519 33.333 0.00 0.00 0.00 4.20
49 50 8.979574 CGCTTTTATATTAGTTTACAGAGGGAG 58.020 37.037 0.00 0.00 0.00 4.30
123 124 1.661341 GCAGGAGTAGGTGCATCTTG 58.339 55.000 3.93 0.00 39.62 3.02
194 235 1.455773 TCCTCGGCATCGATGGACT 60.456 57.895 26.00 0.00 45.04 3.85
243 1080 7.941431 TTCATATTATTTTACAACACCCCGT 57.059 32.000 0.00 0.00 0.00 5.28
250 1087 2.510064 TACAACACCCCGTCCGCATC 62.510 60.000 0.00 0.00 0.00 3.91
313 1150 0.107508 CACTCGGCAGGGATGAACAT 60.108 55.000 0.00 0.00 0.00 2.71
314 1151 0.107508 ACTCGGCAGGGATGAACATG 60.108 55.000 0.00 0.00 0.00 3.21
330 1167 1.368019 ATGCGCGCGATTCGAATTG 60.368 52.632 37.18 19.36 41.67 2.32
357 1197 1.613520 GCCACCAAACCCTACTTCCTC 60.614 57.143 0.00 0.00 0.00 3.71
359 1199 1.985895 CACCAAACCCTACTTCCTCCT 59.014 52.381 0.00 0.00 0.00 3.69
398 1238 0.673985 TGAGGTGACAAGAGGACACG 59.326 55.000 0.00 0.00 35.68 4.49
418 1258 2.095466 CGATCTCTACGCCTGGAATCTC 60.095 54.545 0.00 0.00 0.00 2.75
426 1266 3.335579 ACGCCTGGAATCTCACTTAAAC 58.664 45.455 0.00 0.00 0.00 2.01
428 1268 2.678336 GCCTGGAATCTCACTTAAACCG 59.322 50.000 0.00 0.00 0.00 4.44
530 1400 0.960364 TGCTTTTGTCCTCGGCATCC 60.960 55.000 0.00 0.00 0.00 3.51
552 1422 4.217767 CCATCGACATTCTCCGGATTACTA 59.782 45.833 3.57 0.00 0.00 1.82
553 1423 5.278808 CCATCGACATTCTCCGGATTACTAA 60.279 44.000 3.57 0.00 0.00 2.24
618 1489 4.227134 CTCCCGGTCTCCCATGCG 62.227 72.222 0.00 0.00 0.00 4.73
622 1493 4.552365 CGGTCTCCCATGCGCCAT 62.552 66.667 4.18 0.00 0.00 4.40
625 1496 4.881440 TCTCCCATGCGCCATGCC 62.881 66.667 4.18 0.00 45.60 4.40
635 1506 4.746309 GCCATGCCCAGCTCACCA 62.746 66.667 0.00 0.00 0.00 4.17
636 1507 2.753043 CCATGCCCAGCTCACCAC 60.753 66.667 0.00 0.00 0.00 4.16
637 1508 2.353958 CATGCCCAGCTCACCACT 59.646 61.111 0.00 0.00 0.00 4.00
645 1516 3.775654 GCTCACCACTCCCTCCGG 61.776 72.222 0.00 0.00 0.00 5.14
877 3400 5.850046 TCCTCTCCTCAAGGAAAAAGATT 57.150 39.130 0.00 0.00 44.91 2.40
891 3420 9.987272 AAGGAAAAAGATTGGAGAATAAAGTTG 57.013 29.630 0.00 0.00 0.00 3.16
955 3484 2.625460 CCCATCCAGAAGCCCCCAA 61.625 63.158 0.00 0.00 0.00 4.12
962 3491 4.295199 GAAGCCCCCAACCCCGTT 62.295 66.667 0.00 0.00 0.00 4.44
1012 3548 2.048603 GGAGCAATGGACCAGCACC 61.049 63.158 8.32 7.36 32.16 5.01
1044 3580 1.690633 GGATGTGGAGGGAGAGCCA 60.691 63.158 0.00 0.00 35.15 4.75
1073 3609 2.364317 CAAGGAGGAGGAGGCGGA 60.364 66.667 0.00 0.00 0.00 5.54
1075 3611 4.824515 AGGAGGAGGAGGCGGACG 62.825 72.222 0.00 0.00 0.00 4.79
1098 3634 3.130160 GCGGGCAAGCCTGAAGAG 61.130 66.667 23.58 3.91 45.10 2.85
1101 3637 3.130160 GGCAAGCCTGAAGAGCCG 61.130 66.667 3.29 0.00 35.42 5.52
1102 3638 2.046892 GCAAGCCTGAAGAGCCGA 60.047 61.111 0.00 0.00 0.00 5.54
1183 3779 2.359230 AGCGCAAGGAGGACAAGC 60.359 61.111 11.47 0.00 38.28 4.01
1200 3796 4.135153 CCTGACGGGCTGACGGAG 62.135 72.222 6.18 0.00 38.39 4.63
1266 3919 2.411904 GTGGACAAGTCTGAAGAGCTG 58.588 52.381 0.00 0.00 0.00 4.24
1269 3922 2.323959 GACAAGTCTGAAGAGCTGACG 58.676 52.381 0.00 0.00 46.50 4.35
1316 3969 0.765510 GAGGTGGAGGTGGACAAGTT 59.234 55.000 0.00 0.00 0.00 2.66
1604 4257 0.471780 TCCAGCTCCAAGACCACTGA 60.472 55.000 0.00 0.00 0.00 3.41
1620 4273 6.016108 AGACCACTGACAGAGTAAGTAGTTTC 60.016 42.308 10.08 0.00 31.73 2.78
1708 4365 1.295930 GCACGTACGCGATTTCTGC 60.296 57.895 15.93 12.07 42.00 4.26
1720 4377 2.280628 GATTTCTGCAGGGGTTCTACG 58.719 52.381 15.13 0.00 0.00 3.51
1729 4386 2.345760 GGGTTCTACGTGCGGGAGA 61.346 63.158 0.00 0.00 0.00 3.71
1735 4392 0.386100 CTACGTGCGGGAGATGATCG 60.386 60.000 0.00 0.00 0.00 3.69
1738 4395 1.437573 GTGCGGGAGATGATCGTGA 59.562 57.895 0.00 0.00 0.00 4.35
1741 4398 1.735973 CGGGAGATGATCGTGAGCA 59.264 57.895 0.00 0.00 0.00 4.26
1744 4401 1.069823 GGGAGATGATCGTGAGCATGT 59.930 52.381 5.19 0.87 37.59 3.21
1836 4497 2.034879 GCGTTCAGCCTTGCTAGCA 61.035 57.895 14.93 14.93 36.40 3.49
1847 4508 0.522626 TTGCTAGCACTACGTACGCA 59.477 50.000 19.17 0.23 0.00 5.24
1849 4510 1.268386 TGCTAGCACTACGTACGCATC 60.268 52.381 14.93 0.21 0.00 3.91
1850 4511 1.002684 GCTAGCACTACGTACGCATCT 60.003 52.381 16.72 8.13 0.00 2.90
1868 4529 4.487412 GCGGCAGCAATGGAGCAC 62.487 66.667 3.18 0.00 44.35 4.40
1911 4587 1.572085 CTCGCAGGCTGTCAACTTGG 61.572 60.000 17.16 0.00 0.00 3.61
1968 4654 7.710907 TGTGTATAGCAAAGTGTCTGGATAATC 59.289 37.037 0.00 0.00 0.00 1.75
1973 4659 5.879223 AGCAAAGTGTCTGGATAATCAAGAG 59.121 40.000 0.00 0.00 0.00 2.85
2022 4708 3.755378 ACTTTGACTGATCACATCTTGCC 59.245 43.478 0.00 0.00 33.38 4.52
2035 4721 8.618702 ATCACATCTTGCCATAAGATTAAGAG 57.381 34.615 0.00 0.00 34.96 2.85
2064 4752 5.287226 ACTACTGTGTGTTACTGTGTTAGC 58.713 41.667 0.00 0.00 41.00 3.09
2110 4798 3.753272 TCTGTAAGCTGATTGAAACCTGC 59.247 43.478 0.00 0.00 0.00 4.85
2128 4816 2.602211 CTGCTCAACTTATCTGCTGACG 59.398 50.000 0.00 0.00 0.00 4.35
2167 4855 1.334869 AGCCTTTTTGTCTGTTGCTCG 59.665 47.619 0.00 0.00 0.00 5.03
2178 4868 0.033920 TGTTGCTCGAGTGATGTGCT 59.966 50.000 15.13 0.00 0.00 4.40
2179 4869 0.441533 GTTGCTCGAGTGATGTGCTG 59.558 55.000 15.13 0.00 0.00 4.41
2180 4870 0.033920 TTGCTCGAGTGATGTGCTGT 59.966 50.000 15.13 0.00 0.00 4.40
2181 4871 0.389037 TGCTCGAGTGATGTGCTGTC 60.389 55.000 15.13 0.00 0.00 3.51
2182 4872 1.080995 GCTCGAGTGATGTGCTGTCC 61.081 60.000 15.13 0.00 0.00 4.02
2183 4873 0.459237 CTCGAGTGATGTGCTGTCCC 60.459 60.000 3.62 0.00 0.00 4.46
2184 4874 1.807165 CGAGTGATGTGCTGTCCCG 60.807 63.158 0.00 0.00 0.00 5.14
2200 4890 2.327343 CCGTGTCGGTGGTCTCGTA 61.327 63.158 0.00 0.00 42.73 3.43
2211 4901 4.142534 CGGTGGTCTCGTATTTCAGTAAGA 60.143 45.833 0.00 0.00 0.00 2.10
2240 4930 7.600065 TCTGTGTTGGTACTGTTCTTCTATAC 58.400 38.462 0.00 0.00 0.00 1.47
2241 4931 7.450634 TCTGTGTTGGTACTGTTCTTCTATACT 59.549 37.037 0.00 0.00 0.00 2.12
2258 4950 7.843490 TCTATACTCTGTTGGTATGTTTTGC 57.157 36.000 0.00 0.00 32.85 3.68
2276 4968 0.652071 GCCTGTGTTTTTGCAAGTGC 59.348 50.000 0.00 0.00 42.50 4.40
2323 5015 4.142881 GCTAAAGTTGGCTGTTAGCTACAC 60.143 45.833 7.26 0.00 44.08 2.90
2327 5026 2.235402 GTTGGCTGTTAGCTACACCCTA 59.765 50.000 0.00 0.00 41.99 3.53
2328 5027 1.829222 TGGCTGTTAGCTACACCCTAC 59.171 52.381 0.00 0.00 41.99 3.18
2329 5028 1.829222 GGCTGTTAGCTACACCCTACA 59.171 52.381 0.00 0.00 41.99 2.74
2330 5029 2.159085 GGCTGTTAGCTACACCCTACAG 60.159 54.545 14.13 14.13 41.99 2.74
2331 5030 2.496470 GCTGTTAGCTACACCCTACAGT 59.504 50.000 17.87 0.00 38.45 3.55
2332 5031 3.698040 GCTGTTAGCTACACCCTACAGTA 59.302 47.826 17.87 0.00 38.45 2.74
2333 5032 4.202030 GCTGTTAGCTACACCCTACAGTAG 60.202 50.000 17.87 0.00 38.45 2.57
2334 5033 4.927049 TGTTAGCTACACCCTACAGTAGT 58.073 43.478 6.84 0.00 39.82 2.73
2335 5034 4.946157 TGTTAGCTACACCCTACAGTAGTC 59.054 45.833 6.84 0.00 39.82 2.59
2336 5035 3.733883 AGCTACACCCTACAGTAGTCA 57.266 47.619 6.84 0.00 39.82 3.41
2337 5036 3.622630 AGCTACACCCTACAGTAGTCAG 58.377 50.000 6.84 0.00 39.82 3.51
2340 5039 2.434428 ACACCCTACAGTAGTCAGTCG 58.566 52.381 6.84 0.67 0.00 4.18
2357 5056 0.679505 TCGGTCTGTTTCTCAGGTGG 59.320 55.000 0.00 0.00 43.76 4.61
2363 5062 3.260884 GTCTGTTTCTCAGGTGGTATGGA 59.739 47.826 0.00 0.00 43.76 3.41
2394 5093 7.151308 AGGAAGAGAAAACTATATCATCGCTG 58.849 38.462 0.00 0.00 0.00 5.18
2419 5135 2.416547 GCATTGCGTATGAGTGTCTGTT 59.583 45.455 3.04 0.00 36.26 3.16
2445 5185 8.141268 TCATTTTGTTTTATTTGACTCCTGGTC 58.859 33.333 0.00 0.00 44.70 4.02
2460 5200 0.310543 TGGTCGACTTGTTTGCATGC 59.689 50.000 16.46 11.82 0.00 4.06
2471 5215 1.824224 TTTGCATGCCGGCCATTTGA 61.824 50.000 26.77 3.54 29.71 2.69
2472 5216 2.105528 GCATGCCGGCCATTTGAG 59.894 61.111 26.77 6.72 29.71 3.02
2553 5304 6.372659 TGCAAGAGAAATCTTAAGCAAGGTAG 59.627 38.462 0.00 0.00 32.22 3.18
2554 5305 6.372937 GCAAGAGAAATCTTAAGCAAGGTAGT 59.627 38.462 0.00 0.00 32.22 2.73
2555 5306 7.549488 GCAAGAGAAATCTTAAGCAAGGTAGTA 59.451 37.037 0.00 0.00 32.22 1.82
2556 5307 9.436957 CAAGAGAAATCTTAAGCAAGGTAGTAA 57.563 33.333 0.00 0.00 32.22 2.24
2557 5308 9.438228 AAGAGAAATCTTAAGCAAGGTAGTAAC 57.562 33.333 0.00 0.00 32.22 2.50
2558 5309 8.594550 AGAGAAATCTTAAGCAAGGTAGTAACA 58.405 33.333 0.00 0.00 32.22 2.41
2559 5310 9.384764 GAGAAATCTTAAGCAAGGTAGTAACAT 57.615 33.333 0.00 0.00 32.22 2.71
2560 5311 9.167311 AGAAATCTTAAGCAAGGTAGTAACATG 57.833 33.333 0.00 0.00 32.22 3.21
2673 5427 1.620739 ATCACTCATCAGGCAGCCGT 61.621 55.000 5.55 0.00 0.00 5.68
2676 5430 0.108138 ACTCATCAGGCAGCCGTAAC 60.108 55.000 5.55 0.00 0.00 2.50
2680 5434 1.131126 CATCAGGCAGCCGTAACAAAG 59.869 52.381 5.55 0.00 0.00 2.77
2681 5435 0.107831 TCAGGCAGCCGTAACAAAGT 59.892 50.000 5.55 0.00 0.00 2.66
2758 5514 0.248289 CTAACCGCCCCGAAAAGAGA 59.752 55.000 0.00 0.00 0.00 3.10
2765 5521 2.014857 GCCCCGAAAAGAGAACATACC 58.985 52.381 0.00 0.00 0.00 2.73
2770 5526 3.797256 CCGAAAAGAGAACATACCGCTAG 59.203 47.826 0.00 0.00 0.00 3.42
2771 5527 4.439700 CCGAAAAGAGAACATACCGCTAGA 60.440 45.833 0.00 0.00 0.00 2.43
2802 5566 6.857437 ACCTTTGGGGAAAAAGAGAATATG 57.143 37.500 0.00 0.00 39.12 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 8.480501 TCCCTCTGTAAACTAATATAAAAGCGT 58.519 33.333 0.00 0.00 0.00 5.07
23 24 8.882415 TCCCTCTGTAAACTAATATAAAAGCG 57.118 34.615 0.00 0.00 0.00 4.68
24 25 9.833917 ACTCCCTCTGTAAACTAATATAAAAGC 57.166 33.333 0.00 0.00 0.00 3.51
28 29 9.851686 TCGTACTCCCTCTGTAAACTAATATAA 57.148 33.333 0.00 0.00 0.00 0.98
29 30 9.499479 CTCGTACTCCCTCTGTAAACTAATATA 57.501 37.037 0.00 0.00 0.00 0.86
30 31 8.216423 TCTCGTACTCCCTCTGTAAACTAATAT 58.784 37.037 0.00 0.00 0.00 1.28
31 32 7.568349 TCTCGTACTCCCTCTGTAAACTAATA 58.432 38.462 0.00 0.00 0.00 0.98
32 33 6.421485 TCTCGTACTCCCTCTGTAAACTAAT 58.579 40.000 0.00 0.00 0.00 1.73
33 34 5.809001 TCTCGTACTCCCTCTGTAAACTAA 58.191 41.667 0.00 0.00 0.00 2.24
34 35 5.188555 TCTCTCGTACTCCCTCTGTAAACTA 59.811 44.000 0.00 0.00 0.00 2.24
35 36 4.019501 TCTCTCGTACTCCCTCTGTAAACT 60.020 45.833 0.00 0.00 0.00 2.66
36 37 4.260170 TCTCTCGTACTCCCTCTGTAAAC 58.740 47.826 0.00 0.00 0.00 2.01
37 38 4.564782 TCTCTCGTACTCCCTCTGTAAA 57.435 45.455 0.00 0.00 0.00 2.01
38 39 4.260170 GTTCTCTCGTACTCCCTCTGTAA 58.740 47.826 0.00 0.00 0.00 2.41
39 40 3.262660 TGTTCTCTCGTACTCCCTCTGTA 59.737 47.826 0.00 0.00 0.00 2.74
40 41 2.040012 TGTTCTCTCGTACTCCCTCTGT 59.960 50.000 0.00 0.00 0.00 3.41
41 42 2.680841 CTGTTCTCTCGTACTCCCTCTG 59.319 54.545 0.00 0.00 0.00 3.35
42 43 2.942306 GCTGTTCTCTCGTACTCCCTCT 60.942 54.545 0.00 0.00 0.00 3.69
43 44 1.402613 GCTGTTCTCTCGTACTCCCTC 59.597 57.143 0.00 0.00 0.00 4.30
44 45 1.465794 GCTGTTCTCTCGTACTCCCT 58.534 55.000 0.00 0.00 0.00 4.20
45 46 0.099082 CGCTGTTCTCTCGTACTCCC 59.901 60.000 0.00 0.00 0.00 4.30
46 47 0.803740 ACGCTGTTCTCTCGTACTCC 59.196 55.000 0.00 0.00 34.41 3.85
47 48 2.615489 AACGCTGTTCTCTCGTACTC 57.385 50.000 0.00 0.00 35.18 2.59
48 49 4.395542 AGATAAACGCTGTTCTCTCGTACT 59.604 41.667 0.00 0.00 35.18 2.73
49 50 4.660105 AGATAAACGCTGTTCTCTCGTAC 58.340 43.478 0.00 0.00 35.18 3.67
123 124 3.494378 TCGTCGTCGACCATCCTC 58.506 61.111 19.29 0.00 41.35 3.71
225 266 3.072944 CGGACGGGGTGTTGTAAAATAA 58.927 45.455 0.00 0.00 0.00 1.40
243 1080 1.378646 AGAGTCTCCACGATGCGGA 60.379 57.895 0.00 0.00 0.00 5.54
250 1087 4.384940 TCATAGAGATCAGAGTCTCCACG 58.615 47.826 0.00 0.00 44.55 4.94
296 1133 1.442526 GCATGTTCATCCCTGCCGAG 61.443 60.000 0.00 0.00 0.00 4.63
297 1134 1.451927 GCATGTTCATCCCTGCCGA 60.452 57.895 0.00 0.00 0.00 5.54
298 1135 2.827051 CGCATGTTCATCCCTGCCG 61.827 63.158 0.00 0.00 0.00 5.69
299 1136 3.113745 CGCATGTTCATCCCTGCC 58.886 61.111 0.00 0.00 0.00 4.85
300 1137 2.410469 GCGCATGTTCATCCCTGC 59.590 61.111 0.30 0.00 0.00 4.85
301 1138 2.711311 CGCGCATGTTCATCCCTG 59.289 61.111 8.75 0.00 0.00 4.45
302 1139 3.204827 GCGCGCATGTTCATCCCT 61.205 61.111 29.10 0.00 0.00 4.20
313 1150 2.021243 CAATTCGAATCGCGCGCA 59.979 55.556 32.61 18.69 40.61 6.09
314 1151 2.430080 ATCCAATTCGAATCGCGCGC 62.430 55.000 27.95 23.91 40.61 6.86
330 1167 2.340328 GGGTTTGGTGGCGTGATCC 61.340 63.158 0.00 0.00 0.00 3.36
357 1197 7.120432 CCTCAGGAAATTCTCTTCTTTTGTAGG 59.880 40.741 0.00 0.00 0.00 3.18
359 1199 7.445402 CACCTCAGGAAATTCTCTTCTTTTGTA 59.555 37.037 0.00 0.00 0.00 2.41
398 1238 2.887783 TGAGATTCCAGGCGTAGAGATC 59.112 50.000 0.00 0.00 0.00 2.75
418 1258 2.737252 GCTGTTCTCTCCGGTTTAAGTG 59.263 50.000 0.00 0.00 0.00 3.16
426 1266 2.159226 AGATAAACGCTGTTCTCTCCGG 60.159 50.000 0.00 0.00 0.00 5.14
428 1268 4.495422 TCAAGATAAACGCTGTTCTCTCC 58.505 43.478 0.00 0.00 0.00 3.71
530 1400 4.244425 AGTAATCCGGAGAATGTCGATG 57.756 45.455 11.34 0.00 0.00 3.84
618 1489 4.746309 TGGTGAGCTGGGCATGGC 62.746 66.667 11.56 11.56 0.00 4.40
620 1491 1.748122 GAGTGGTGAGCTGGGCATG 60.748 63.158 0.00 0.00 0.00 4.06
621 1492 2.673523 GAGTGGTGAGCTGGGCAT 59.326 61.111 0.00 0.00 0.00 4.40
622 1493 3.640407 GGAGTGGTGAGCTGGGCA 61.640 66.667 0.00 0.00 0.00 5.36
625 1496 2.664081 GGAGGGAGTGGTGAGCTGG 61.664 68.421 0.00 0.00 0.00 4.85
626 1497 2.985456 GGAGGGAGTGGTGAGCTG 59.015 66.667 0.00 0.00 0.00 4.24
708 3231 1.076705 GTCTTCCAGGAATGCCCCC 60.077 63.158 1.09 0.00 34.66 5.40
839 3362 1.823899 GGATGGATTGGGTGCCGTC 60.824 63.158 0.00 0.00 39.06 4.79
877 3400 5.995282 TCGCTTTCTTCAACTTTATTCTCCA 59.005 36.000 0.00 0.00 0.00 3.86
891 3420 4.056050 TGGTCTACTGTTTCGCTTTCTTC 58.944 43.478 0.00 0.00 0.00 2.87
976 3505 3.724914 CTCCGCTCCGCTTCTTCCC 62.725 68.421 0.00 0.00 0.00 3.97
986 3515 2.203126 CCATTGCTCCTCCGCTCC 60.203 66.667 0.00 0.00 0.00 4.70
987 3516 1.522580 GTCCATTGCTCCTCCGCTC 60.523 63.158 0.00 0.00 0.00 5.03
1012 3548 1.270414 ACATCCACCTCCAGCTCCTG 61.270 60.000 0.00 0.00 0.00 3.86
1044 3580 1.448540 CTCCTTGCGCTGATCCGTT 60.449 57.895 9.73 0.00 0.00 4.44
1101 3637 1.880340 CTCCTTGCGCTGATCCGTC 60.880 63.158 9.73 0.00 0.00 4.79
1102 3638 2.185350 CTCCTTGCGCTGATCCGT 59.815 61.111 9.73 0.00 0.00 4.69
1183 3779 4.135153 CTCCGTCAGCCCGTCAGG 62.135 72.222 0.00 0.00 39.47 3.86
1295 3948 1.074090 TTGTCCACCTCCACCTCCA 60.074 57.895 0.00 0.00 0.00 3.86
1316 3969 0.318441 CTGGTCGGTGAGCTCTTCAA 59.682 55.000 16.19 0.00 37.61 2.69
1352 4005 0.247736 CTCCTTGTCCTTGTCCTCCG 59.752 60.000 0.00 0.00 0.00 4.63
1359 4012 1.203523 CTCTCCGTCTCCTTGTCCTTG 59.796 57.143 0.00 0.00 0.00 3.61
1392 4045 3.041627 GAAGAGCGACGGCGACTCT 62.042 63.158 25.37 25.37 45.81 3.24
1527 4180 1.542915 TCTTCCCGTGACGAGTTAAGG 59.457 52.381 6.54 0.00 0.00 2.69
1565 4218 2.022240 GATCTCCCTGGTCCTGACGC 62.022 65.000 0.00 0.00 0.00 5.19
1567 4220 1.408969 GAGATCTCCCTGGTCCTGAC 58.591 60.000 12.00 0.00 0.00 3.51
1589 4242 0.681733 TCTGTCAGTGGTCTTGGAGC 59.318 55.000 0.00 0.00 0.00 4.70
1590 4243 1.967066 ACTCTGTCAGTGGTCTTGGAG 59.033 52.381 6.84 0.00 32.26 3.86
1591 4244 2.088104 ACTCTGTCAGTGGTCTTGGA 57.912 50.000 6.84 0.00 32.26 3.53
1594 4247 5.386924 ACTACTTACTCTGTCAGTGGTCTT 58.613 41.667 6.84 0.00 36.43 3.01
1595 4248 4.988029 ACTACTTACTCTGTCAGTGGTCT 58.012 43.478 6.84 0.00 36.43 3.85
1596 4249 5.708877 AACTACTTACTCTGTCAGTGGTC 57.291 43.478 6.84 0.00 32.00 4.02
1604 4257 8.803397 AAAAACTTGGAAACTACTTACTCTGT 57.197 30.769 0.00 0.00 0.00 3.41
1708 4365 2.125673 CCGCACGTAGAACCCCTG 60.126 66.667 0.00 0.00 0.00 4.45
1720 4377 0.596083 CTCACGATCATCTCCCGCAC 60.596 60.000 0.00 0.00 0.00 5.34
1729 4386 0.816825 GCCCACATGCTCACGATCAT 60.817 55.000 0.00 0.00 0.00 2.45
1735 4392 3.434319 CACCGCCCACATGCTCAC 61.434 66.667 0.00 0.00 0.00 3.51
1738 4395 4.415150 CCTCACCGCCCACATGCT 62.415 66.667 0.00 0.00 0.00 3.79
1741 4398 3.402681 CCTCCTCACCGCCCACAT 61.403 66.667 0.00 0.00 0.00 3.21
1856 4517 0.528924 TACGTACGTGCTCCATTGCT 59.471 50.000 30.25 1.29 0.00 3.91
1894 4555 2.620112 CCCAAGTTGACAGCCTGCG 61.620 63.158 3.87 0.00 0.00 5.18
1911 4587 0.961753 CCAAAGGTCACCTGCTTTCC 59.038 55.000 0.00 0.00 32.13 3.13
1968 4654 4.926238 AGAACGTCAGCACTTAATCTCTTG 59.074 41.667 0.00 0.00 0.00 3.02
1973 4659 4.947420 GTGAAGAACGTCAGCACTTAATC 58.053 43.478 0.00 0.00 0.00 1.75
2004 4690 3.639672 ATGGCAAGATGTGATCAGTCA 57.360 42.857 0.00 0.00 0.00 3.41
2035 4721 6.976925 ACACAGTAACACACAGTAGTTCTTAC 59.023 38.462 0.00 0.00 0.00 2.34
2110 4798 3.369147 CCAACGTCAGCAGATAAGTTGAG 59.631 47.826 19.03 10.34 38.03 3.02
2128 4816 3.683340 GGCTGTAGCAGTTAACTACCAAC 59.317 47.826 8.04 5.02 44.36 3.77
2167 4855 1.016130 CACGGGACAGCACATCACTC 61.016 60.000 0.00 0.00 0.00 3.51
2183 4873 0.169672 AATACGAGACCACCGACACG 59.830 55.000 0.00 0.00 0.00 4.49
2184 4874 2.257034 GAAATACGAGACCACCGACAC 58.743 52.381 0.00 0.00 0.00 3.67
2200 4890 6.828785 ACCAACACAGAGTTTCTTACTGAAAT 59.171 34.615 0.00 0.00 45.19 2.17
2211 4901 5.099042 AGAACAGTACCAACACAGAGTTT 57.901 39.130 0.00 0.00 38.74 2.66
2240 4930 3.569701 ACAGGCAAAACATACCAACAGAG 59.430 43.478 0.00 0.00 0.00 3.35
2241 4931 3.317711 CACAGGCAAAACATACCAACAGA 59.682 43.478 0.00 0.00 0.00 3.41
2276 4968 3.859386 GTCAAGTTCAGGTTTGCACTTTG 59.141 43.478 0.00 0.00 38.47 2.77
2277 4969 3.763897 AGTCAAGTTCAGGTTTGCACTTT 59.236 39.130 0.00 0.00 38.47 2.66
2278 4970 3.129287 CAGTCAAGTTCAGGTTTGCACTT 59.871 43.478 0.00 0.00 40.66 3.16
2279 4971 2.684881 CAGTCAAGTTCAGGTTTGCACT 59.315 45.455 0.00 0.00 31.89 4.40
2280 4972 2.796032 GCAGTCAAGTTCAGGTTTGCAC 60.796 50.000 0.00 0.00 0.00 4.57
2281 4973 1.405105 GCAGTCAAGTTCAGGTTTGCA 59.595 47.619 0.00 0.00 0.00 4.08
2282 4974 1.678101 AGCAGTCAAGTTCAGGTTTGC 59.322 47.619 0.00 0.00 0.00 3.68
2323 5015 2.015587 GACCGACTGACTACTGTAGGG 58.984 57.143 18.38 10.98 41.95 3.53
2357 5056 8.397575 AGTTTTCTCTTCCTCTTTTTCCATAC 57.602 34.615 0.00 0.00 0.00 2.39
2394 5093 0.378257 CACTCATACGCAATGCACCC 59.622 55.000 5.91 0.00 35.38 4.61
2419 5135 8.017418 ACCAGGAGTCAAATAAAACAAAATGA 57.983 30.769 0.00 0.00 0.00 2.57
2445 5185 1.442520 CCGGCATGCAAACAAGTCG 60.443 57.895 21.36 10.79 41.94 4.18
2452 5192 1.375652 CAAATGGCCGGCATGCAAA 60.376 52.632 30.85 6.18 0.00 3.68
2460 5200 1.452108 GGTCTCCTCAAATGGCCGG 60.452 63.158 0.00 0.00 0.00 6.13
2471 5215 1.884497 CGGATGATCTAGCGGTCTCCT 60.884 57.143 0.00 0.00 0.00 3.69
2472 5216 0.523966 CGGATGATCTAGCGGTCTCC 59.476 60.000 0.00 0.00 0.00 3.71
2504 5248 9.245481 GCAATAACCTACTCCTACTAGTATGAT 57.755 37.037 2.33 0.32 31.70 2.45
2506 5250 8.405418 TGCAATAACCTACTCCTACTAGTATG 57.595 38.462 2.33 0.51 31.70 2.39
2507 5251 9.080097 CTTGCAATAACCTACTCCTACTAGTAT 57.920 37.037 2.33 0.00 31.70 2.12
2508 5252 8.277197 TCTTGCAATAACCTACTCCTACTAGTA 58.723 37.037 0.00 1.89 0.00 1.82
2509 5253 7.124052 TCTTGCAATAACCTACTCCTACTAGT 58.876 38.462 0.00 0.00 0.00 2.57
2510 5254 7.502895 TCTCTTGCAATAACCTACTCCTACTAG 59.497 40.741 0.00 0.00 0.00 2.57
2673 5427 4.124238 GCACTGGTCAGTACACTTTGTTA 58.876 43.478 3.06 0.00 40.20 2.41
2676 5430 2.560504 TGCACTGGTCAGTACACTTTG 58.439 47.619 3.06 0.00 40.20 2.77
2680 5434 1.442769 CCATGCACTGGTCAGTACAC 58.557 55.000 6.21 0.00 37.51 2.90
2681 5435 0.324614 CCCATGCACTGGTCAGTACA 59.675 55.000 6.50 6.50 44.30 2.90
2779 5535 6.322931 ACATATTCTCTTTTTCCCCAAAGGT 58.677 36.000 0.00 0.00 34.90 3.50
2780 5536 6.437162 TGACATATTCTCTTTTTCCCCAAAGG 59.563 38.462 0.00 0.00 34.90 3.11
2785 5541 7.703058 TCTTTGACATATTCTCTTTTTCCCC 57.297 36.000 0.00 0.00 0.00 4.81
2788 5544 9.630098 TTGCATCTTTGACATATTCTCTTTTTC 57.370 29.630 0.00 0.00 0.00 2.29
2793 5557 7.934855 ACTTTGCATCTTTGACATATTCTCT 57.065 32.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.