Multiple sequence alignment - TraesCS5A01G350700

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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 TraesCS5A01G350700 chr5A 100.000 3050 0 0 1 3050 553426272 553423223 0.000000e+00 5633.0
1 TraesCS5A01G350700 chr5A 84.586 1291 161 11 1 1254 553465065 553463776 0.000000e+00 1247.0
2 TraesCS5A01G350700 chr5A 81.758 455 51 14 2607 3050 553458493 553458060 4.840000e-93 351.0
3 TraesCS5A01G350700 chr5A 91.398 186 16 0 2021 2206 553462500 553462315 3.900000e-64 255.0
4 TraesCS5A01G350700 chr5A 88.554 166 18 1 1859 2023 553462882 553462717 1.850000e-47 200.0
5 TraesCS5A01G350700 chr5A 87.342 158 16 3 1612 1766 553463385 553463229 8.690000e-41 178.0
6 TraesCS5A01G350700 chr5B 88.481 1797 162 19 1 1764 532895570 532893786 0.000000e+00 2130.0
7 TraesCS5A01G350700 chr5B 88.418 1062 68 21 2019 3045 532892216 532891175 0.000000e+00 1229.0
8 TraesCS5A01G350700 chr5B 83.861 1295 166 14 1 1254 532935259 532933967 0.000000e+00 1194.0
9 TraesCS5A01G350700 chr5B 79.869 765 121 11 10 753 532890046 532889294 2.080000e-146 529.0
10 TraesCS5A01G350700 chr5B 76.177 1062 167 46 741 1764 532888353 532887340 5.910000e-132 481.0
11 TraesCS5A01G350700 chr5B 89.595 346 36 0 2591 2936 532878309 532877964 1.000000e-119 440.0
12 TraesCS5A01G350700 chr5B 83.434 495 60 10 2019 2498 532932931 532932444 1.000000e-119 440.0
13 TraesCS5A01G350700 chr5B 83.040 454 53 13 2610 3050 532932318 532931876 1.030000e-104 390.0
14 TraesCS5A01G350700 chr5B 81.529 471 66 14 2019 2476 532878852 532878390 4.800000e-98 368.0
15 TraesCS5A01G350700 chr5B 79.861 432 64 20 1612 2023 532933577 532933149 8.270000e-76 294.0
16 TraesCS5A01G350700 chr5D 84.071 1513 179 26 1 1472 438372466 438370975 0.000000e+00 1402.0
17 TraesCS5A01G350700 chr5D 83.966 1291 169 10 1 1254 438390525 438389236 0.000000e+00 1203.0
18 TraesCS5A01G350700 chr5D 79.518 1079 131 49 2019 3050 438388209 438387174 0.000000e+00 686.0
19 TraesCS5A01G350700 chr5D 78.631 1081 166 35 2019 3050 438370186 438369122 0.000000e+00 656.0
20 TraesCS5A01G350700 chr5D 78.915 1124 120 47 228 1332 438364930 438363905 0.000000e+00 654.0
21 TraesCS5A01G350700 chr5D 89.174 351 38 0 2586 2936 438361640 438361290 3.610000e-119 438.0
22 TraesCS5A01G350700 chr5D 81.489 470 70 12 2019 2479 438362236 438361775 1.340000e-98 370.0
23 TraesCS5A01G350700 chr5D 80.742 431 57 22 1612 2023 438388851 438388428 2.280000e-81 313.0
24 TraesCS5A01G350700 chr1D 79.492 1063 179 24 227 1259 420860419 420859366 0.000000e+00 719.0
25 TraesCS5A01G350700 chr1D 78.316 475 86 12 2019 2479 420856755 420856284 1.070000e-74 291.0
26 TraesCS5A01G350700 chr1D 89.583 48 5 0 2366 2413 399188630 399188583 9.130000e-06 62.1
27 TraesCS5A01G350700 chr1B 77.331 547 97 20 2019 2548 569561870 569561334 6.390000e-77 298.0
28 TraesCS5A01G350700 chr1B 87.958 191 21 2 2599 2788 569561312 569561123 1.100000e-54 224.0
29 TraesCS5A01G350700 chr7B 95.238 42 2 0 395 436 616903550 616903591 1.960000e-07 67.6
30 TraesCS5A01G350700 chr6D 77.119 118 23 2 1908 2023 362987967 362988082 7.060000e-07 65.8
31 TraesCS5A01G350700 chr6B 77.119 118 23 2 1908 2023 544403615 544403730 7.060000e-07 65.8
32 TraesCS5A01G350700 chr6A 77.119 118 23 2 1908 2023 503426228 503426343 7.060000e-07 65.8


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 TraesCS5A01G350700 chr5A 553423223 553426272 3049 True 5633.000000 5633 100.000000 1 3050 1 chr5A.!!$R1 3049
1 TraesCS5A01G350700 chr5A 553458060 553465065 7005 True 446.200000 1247 86.727600 1 3050 5 chr5A.!!$R2 3049
2 TraesCS5A01G350700 chr5B 532887340 532895570 8230 True 1092.250000 2130 83.236250 1 3045 4 chr5B.!!$R2 3044
3 TraesCS5A01G350700 chr5B 532931876 532935259 3383 True 579.500000 1194 82.549000 1 3050 4 chr5B.!!$R3 3049
4 TraesCS5A01G350700 chr5B 532877964 532878852 888 True 404.000000 440 85.562000 2019 2936 2 chr5B.!!$R1 917
5 TraesCS5A01G350700 chr5D 438369122 438372466 3344 True 1029.000000 1402 81.351000 1 3050 2 chr5D.!!$R2 3049
6 TraesCS5A01G350700 chr5D 438387174 438390525 3351 True 734.000000 1203 81.408667 1 3050 3 chr5D.!!$R3 3049
7 TraesCS5A01G350700 chr5D 438361290 438364930 3640 True 487.333333 654 83.192667 228 2936 3 chr5D.!!$R1 2708
8 TraesCS5A01G350700 chr1D 420856284 420860419 4135 True 505.000000 719 78.904000 227 2479 2 chr1D.!!$R2 2252
9 TraesCS5A01G350700 chr1B 569561123 569561870 747 True 261.000000 298 82.644500 2019 2788 2 chr1B.!!$R1 769

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
408 445 0.035317 TTGTGTGGCAGAGCTTCGAT 59.965 50.0 0.0 0.0 0.0 3.59 F
1385 2643 0.322906 GAAACTCCAGCAGAAGGGGG 60.323 60.0 0.0 0.0 0.0 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 6414 0.611714 GGTCCCTGTGTATCACCGTT 59.388 55.0 0.00 0.0 32.73 4.44 R
2887 10864 0.392863 TCATGGTCATGGCGTTCCTG 60.393 55.0 10.61 0.0 39.24 3.86 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
54 55 3.249189 TCGGCCAAGGACCAGCTT 61.249 61.111 2.24 0.00 0.00 3.74
122 123 3.889044 CGCCTTCGCTCTCGGCTA 61.889 66.667 0.00 0.00 41.61 3.93
141 142 2.599281 TTCTCCCCAGACGACGCA 60.599 61.111 0.00 0.00 0.00 5.24
328 350 4.121669 GCAGCTCGTCCTCGCAGA 62.122 66.667 0.00 0.00 36.96 4.26
408 445 0.035317 TTGTGTGGCAGAGCTTCGAT 59.965 50.000 0.00 0.00 0.00 3.59
454 491 0.532417 GATGAAGATGCGGCTGAGCT 60.532 55.000 3.72 0.00 38.13 4.09
549 586 3.625897 CTGGACCCCAGCACGTCA 61.626 66.667 0.00 0.00 45.13 4.35
551 588 3.936203 GGACCCCAGCACGTCACA 61.936 66.667 0.00 0.00 0.00 3.58
620 657 0.968901 TGGAGGAGTTACGCCGTGAT 60.969 55.000 0.00 0.00 0.00 3.06
684 721 2.278206 CGCACGGACGAGGAGATG 60.278 66.667 0.00 0.00 34.06 2.90
692 729 1.115467 GACGAGGAGATGTCCATGGT 58.885 55.000 12.58 5.47 46.80 3.55
738 775 4.150203 ACGCGGTGTGTGGTGACA 62.150 61.111 12.47 0.00 38.70 3.58
1042 1100 2.160205 ACAAGTTCTCGATCGACTCCA 58.840 47.619 15.15 0.00 0.00 3.86
1043 1101 2.095161 ACAAGTTCTCGATCGACTCCAC 60.095 50.000 15.15 8.28 0.00 4.02
1132 1190 4.614112 ACGTGCAGAGCAGCAGCA 62.614 61.111 3.17 3.36 46.69 4.41
1135 1193 2.668550 TGCAGAGCAGCAGCACAG 60.669 61.111 3.17 0.00 45.49 3.66
1137 1195 1.745864 GCAGAGCAGCAGCACAGAT 60.746 57.895 3.17 0.00 45.49 2.90
1141 1199 3.823330 GCAGCAGCACAGATGGCC 61.823 66.667 0.00 0.00 41.58 5.36
1194 1252 0.523335 TCGTCGACGCACAGATGATG 60.523 55.000 32.19 2.59 39.60 3.07
1355 2587 4.796495 CCGGTGTTAGCCCTGCCC 62.796 72.222 0.00 0.00 0.00 5.36
1370 2628 1.880027 CTGCCCAACACAGGTAGAAAC 59.120 52.381 0.00 0.00 39.28 2.78
1381 2639 3.007398 ACAGGTAGAAACTCCAGCAGAAG 59.993 47.826 0.00 0.00 0.00 2.85
1382 2640 2.569404 AGGTAGAAACTCCAGCAGAAGG 59.431 50.000 0.00 0.00 0.00 3.46
1384 2642 0.695347 AGAAACTCCAGCAGAAGGGG 59.305 55.000 0.00 0.00 0.00 4.79
1385 2643 0.322906 GAAACTCCAGCAGAAGGGGG 60.323 60.000 0.00 0.00 0.00 5.40
1410 2680 2.272146 CAGCCCTGCCGGTGTTAT 59.728 61.111 1.90 0.00 0.00 1.89
1439 2709 1.992667 CTGCTGCTCACATGCATTTTG 59.007 47.619 0.00 0.00 42.48 2.44
1485 2920 6.934645 CAGAGGTACAGTTGTATTTTCTTCCA 59.065 38.462 0.00 0.00 32.54 3.53
1490 2925 9.758651 GGTACAGTTGTATTTTCTTCCATTTTT 57.241 29.630 0.00 0.00 32.54 1.94
1524 2976 2.614779 ACTCTGAACATGTGATGCTCG 58.385 47.619 0.00 0.00 0.00 5.03
1534 3092 4.880120 ACATGTGATGCTCGATCATTCTTT 59.120 37.500 2.84 0.00 43.20 2.52
1535 3093 5.007430 ACATGTGATGCTCGATCATTCTTTC 59.993 40.000 2.84 0.00 43.20 2.62
1537 3121 4.330894 TGTGATGCTCGATCATTCTTTCAC 59.669 41.667 11.23 11.23 43.20 3.18
1541 3125 3.433274 TGCTCGATCATTCTTTCACACAC 59.567 43.478 0.00 0.00 0.00 3.82
1543 3127 4.667668 GCTCGATCATTCTTTCACACACAC 60.668 45.833 0.00 0.00 0.00 3.82
1577 3305 1.337703 TCACAGCACCAATTTCACAGC 59.662 47.619 0.00 0.00 0.00 4.40
1591 3319 2.586425 TCACAGCCAAGGGAAGAAAAG 58.414 47.619 0.00 0.00 0.00 2.27
1603 3340 2.087646 GAAGAAAAGCCGAGAGCCAAT 58.912 47.619 0.00 0.00 45.47 3.16
1606 3343 3.209410 AGAAAAGCCGAGAGCCAATATG 58.791 45.455 0.00 0.00 45.47 1.78
1610 3377 2.042464 AGCCGAGAGCCAATATGAGAA 58.958 47.619 0.00 0.00 45.47 2.87
1637 3408 1.071605 ACGTCGAGCAAAATCAGAGC 58.928 50.000 0.00 0.00 0.00 4.09
1646 3417 4.077108 AGCAAAATCAGAGCAGATCACAA 58.923 39.130 0.00 0.00 0.00 3.33
1723 3494 4.339247 ACAACTTCTCCAAAACACTCATGG 59.661 41.667 0.00 0.00 35.49 3.66
1759 3530 1.754803 TCGGCATGGTCTACAAGGTAG 59.245 52.381 0.00 0.00 0.00 3.18
1764 3535 4.891756 GGCATGGTCTACAAGGTAGTACTA 59.108 45.833 0.00 0.00 0.00 1.82
1767 3538 6.679884 GCATGGTCTACAAGGTAGTACTACAC 60.680 46.154 29.38 19.97 37.78 2.90
1774 3545 9.231297 TCTACAAGGTAGTACTACACGTTTTAT 57.769 33.333 29.38 10.88 37.78 1.40
1777 3548 7.039784 ACAAGGTAGTACTACACGTTTTATCCA 60.040 37.037 29.38 0.00 37.78 3.41
1783 4769 8.080083 AGTACTACACGTTTTATCCACTTTTG 57.920 34.615 0.00 0.00 0.00 2.44
1806 4792 5.071250 TGCTAACTTTCAGTCCCTTGAACTA 59.929 40.000 0.00 0.00 36.84 2.24
1808 4794 5.367945 AACTTTCAGTCCCTTGAACTACA 57.632 39.130 0.00 0.00 36.84 2.74
1814 5139 8.754991 TTTCAGTCCCTTGAACTACAAAAATA 57.245 30.769 0.00 0.00 36.84 1.40
1820 5145 7.227910 GTCCCTTGAACTACAAAAATACAGTCA 59.772 37.037 0.00 0.00 38.08 3.41
1842 5415 8.872845 AGTCAAACAATTTCAACAGCTAAAAAG 58.127 29.630 0.00 0.00 0.00 2.27
1845 5418 6.833342 ACAATTTCAACAGCTAAAAAGCAG 57.167 33.333 0.00 0.00 37.25 4.24
1848 5421 7.010460 ACAATTTCAACAGCTAAAAAGCAGTTC 59.990 33.333 5.33 0.00 41.46 3.01
1850 5423 5.574891 TCAACAGCTAAAAAGCAGTTCAA 57.425 34.783 5.33 0.00 41.46 2.69
1851 5424 5.960113 TCAACAGCTAAAAAGCAGTTCAAA 58.040 33.333 5.33 0.00 41.46 2.69
1854 5427 7.222611 TCAACAGCTAAAAAGCAGTTCAAAATC 59.777 33.333 5.33 0.00 41.46 2.17
1855 5428 6.809869 ACAGCTAAAAAGCAGTTCAAAATCT 58.190 32.000 0.00 0.00 37.25 2.40
1857 5430 8.413229 ACAGCTAAAAAGCAGTTCAAAATCTTA 58.587 29.630 0.00 0.00 37.25 2.10
1859 5432 8.633561 AGCTAAAAAGCAGTTCAAAATCTTACT 58.366 29.630 0.00 0.00 37.25 2.24
1864 5437 6.699575 AGCAGTTCAAAATCTTACTTGTGT 57.300 33.333 0.00 0.00 0.00 3.72
1865 5438 6.729187 AGCAGTTCAAAATCTTACTTGTGTC 58.271 36.000 0.00 0.00 0.00 3.67
1893 5495 4.232820 ACCATTGGGAAGGGAACATTAGAT 59.767 41.667 7.78 0.00 35.48 1.98
1905 5507 1.139058 ACATTAGATGGCGGTCAGGTC 59.861 52.381 0.00 0.00 33.60 3.85
1962 5564 2.238395 GGGAGCAGAGGAGTTCAAGAAT 59.762 50.000 0.00 0.00 0.00 2.40
2048 6414 0.622136 TACACCAGGACTCGAGGCTA 59.378 55.000 19.83 0.00 0.00 3.93
2081 6447 1.000396 GGACCTCAAGGCCAGCAAT 60.000 57.895 5.01 0.00 39.32 3.56
2084 6450 0.698238 ACCTCAAGGCCAGCAATGTA 59.302 50.000 5.01 0.00 39.32 2.29
2085 6451 1.285962 ACCTCAAGGCCAGCAATGTAT 59.714 47.619 5.01 0.00 39.32 2.29
2296 6710 3.425162 AATGTGGAACCTCTTCTGACC 57.575 47.619 0.00 0.00 34.36 4.02
2356 6774 1.227089 CTCGATGGAGGGCGTCTTG 60.227 63.158 7.19 0.00 36.61 3.02
2364 6782 2.737376 GGGCGTCTTGTCGGTCAC 60.737 66.667 0.00 0.00 0.00 3.67
2423 6841 0.941463 CGTGAGCGGCATCAGGATAC 60.941 60.000 1.45 0.00 37.27 2.24
2481 6903 6.108687 TGACAATCTATGTAAGCACCTGAAG 58.891 40.000 0.00 0.00 44.12 3.02
2504 6926 4.420522 AAAACTGACAATGCCAAACCAT 57.579 36.364 0.00 0.00 0.00 3.55
2686 10651 1.938926 GCAGAGAGCTGTTCACAGGAC 60.939 57.143 9.01 0.00 44.17 3.85
2869 10843 0.178921 TGGGAGACAAGAGCCAGAGT 60.179 55.000 0.00 0.00 0.00 3.24
2887 10864 1.671845 AGTAGCGATCTCGAGAACACC 59.328 52.381 20.91 10.45 43.02 4.16
2888 10865 1.400846 GTAGCGATCTCGAGAACACCA 59.599 52.381 20.91 2.14 43.02 4.17
2889 10866 0.453793 AGCGATCTCGAGAACACCAG 59.546 55.000 20.91 5.11 43.02 4.00
2936 10933 0.455005 GGGACGGTAGTACAGCAGTC 59.545 60.000 2.06 10.01 31.06 3.51
2940 10937 2.230750 GACGGTAGTACAGCAGTCCTTT 59.769 50.000 2.06 0.00 0.00 3.11
2941 10938 2.631545 ACGGTAGTACAGCAGTCCTTTT 59.368 45.455 2.06 0.00 0.00 2.27
2944 10941 4.246458 GGTAGTACAGCAGTCCTTTTCAG 58.754 47.826 2.06 0.00 0.00 3.02
2951 10948 1.819305 GCAGTCCTTTTCAGGGAAGCA 60.819 52.381 0.00 0.00 41.25 3.91
2957 10954 1.538950 CTTTTCAGGGAAGCAGCACTC 59.461 52.381 0.00 0.00 0.00 3.51
3024 11027 8.549548 CAGATTTGTAGAGCATTTATCACAGAG 58.450 37.037 0.00 0.00 0.00 3.35
3026 11029 8.659925 ATTTGTAGAGCATTTATCACAGAGAG 57.340 34.615 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 2.637383 GCGTCGTCTGGGGAGAAGT 61.637 63.158 0.00 0.00 0.00 3.01
165 166 0.105224 TGCCGTTGTACCATATCCCG 59.895 55.000 0.00 0.00 0.00 5.14
168 169 2.812011 GGGAATGCCGTTGTACCATATC 59.188 50.000 0.00 0.00 33.83 1.63
345 382 4.675029 AGGTTGCCGTCGTTCCCG 62.675 66.667 0.00 0.00 0.00 5.14
346 383 3.047877 CAGGTTGCCGTCGTTCCC 61.048 66.667 0.00 0.00 0.00 3.97
375 412 2.590575 ACAACCGTGCCGTCCAAG 60.591 61.111 0.00 0.00 0.00 3.61
376 413 2.897846 CACAACCGTGCCGTCCAA 60.898 61.111 0.00 0.00 36.06 3.53
390 427 0.390340 GATCGAAGCTCTGCCACACA 60.390 55.000 0.00 0.00 0.00 3.72
510 547 3.324108 TAGGAAAAGCGCCCCGGT 61.324 61.111 2.29 0.00 40.00 5.28
605 642 1.146358 GCTGATCACGGCGTAACTCC 61.146 60.000 14.22 0.95 38.67 3.85
607 644 4.496670 GCTGATCACGGCGTAACT 57.503 55.556 14.22 0.00 38.67 2.24
620 657 1.805539 GCGCTGACGTACATGCTGA 60.806 57.895 0.00 0.00 42.83 4.26
645 682 2.682952 CGATCGCCGTGTAGATTACT 57.317 50.000 0.26 0.00 0.00 2.24
668 705 1.226717 GACATCTCCTCGTCCGTGC 60.227 63.158 0.00 0.00 0.00 5.34
684 721 0.537188 AGACGGTGATGACCATGGAC 59.463 55.000 21.47 13.94 43.33 4.02
720 757 3.335534 GTCACCACACACCGCGTC 61.336 66.667 4.92 0.00 0.00 5.19
728 765 1.961277 CCGGAGCTTGTCACCACAC 60.961 63.158 0.00 0.00 29.76 3.82
729 766 2.425592 CCGGAGCTTGTCACCACA 59.574 61.111 0.00 0.00 0.00 4.17
738 775 2.829384 TTGGAACCTGCCGGAGCTT 61.829 57.895 5.05 0.00 40.80 3.74
1132 1190 2.040813 ACTTGATCAGTTGGCCATCTGT 59.959 45.455 32.94 23.69 33.89 3.41
1134 1192 2.719739 CACTTGATCAGTTGGCCATCT 58.280 47.619 6.09 8.83 30.92 2.90
1135 1193 1.133790 GCACTTGATCAGTTGGCCATC 59.866 52.381 6.09 5.81 30.92 3.51
1137 1195 1.236616 CGCACTTGATCAGTTGGCCA 61.237 55.000 0.00 0.00 30.92 5.36
1141 1199 1.069703 CACCACGCACTTGATCAGTTG 60.070 52.381 0.00 0.00 30.92 3.16
1167 1225 4.539881 GCGTCGACGAGCTCCTCC 62.540 72.222 39.74 16.64 43.02 4.30
1169 1227 4.104417 GTGCGTCGACGAGCTCCT 62.104 66.667 39.74 0.00 43.02 3.69
1332 2564 3.431725 GGCTAACACCGGCACTGC 61.432 66.667 0.00 0.00 0.00 4.40
1355 2587 2.808543 GCTGGAGTTTCTACCTGTGTTG 59.191 50.000 0.00 0.00 0.00 3.33
1382 2640 2.936032 AGGGCTGTCTTCACCCCC 60.936 66.667 0.00 0.00 45.48 5.40
1384 2642 2.360475 GCAGGGCTGTCTTCACCC 60.360 66.667 0.00 0.00 44.62 4.61
1385 2643 2.360475 GGCAGGGCTGTCTTCACC 60.360 66.667 0.00 0.00 31.34 4.02
1393 2663 1.819632 GATAACACCGGCAGGGCTG 60.820 63.158 8.08 0.00 43.47 4.85
1410 2680 1.984026 TGAGCAGCAGGACGGATGA 60.984 57.895 0.00 0.00 0.00 2.92
1439 2709 6.173339 TCTGAATCTCCAGAACCATACAAAC 58.827 40.000 0.00 0.00 39.96 2.93
1497 2932 8.743085 AGCATCACATGTTCAGAGTTATTAAT 57.257 30.769 0.00 0.00 0.00 1.40
1498 2933 7.010460 CGAGCATCACATGTTCAGAGTTATTAA 59.990 37.037 0.00 0.00 40.07 1.40
1499 2934 6.476706 CGAGCATCACATGTTCAGAGTTATTA 59.523 38.462 0.00 0.00 40.07 0.98
1501 2936 4.807834 CGAGCATCACATGTTCAGAGTTAT 59.192 41.667 0.00 0.00 40.07 1.89
1502 2937 4.082245 TCGAGCATCACATGTTCAGAGTTA 60.082 41.667 0.00 0.00 40.07 2.24
1503 2938 2.998670 CGAGCATCACATGTTCAGAGTT 59.001 45.455 0.00 0.00 40.07 3.01
1504 2939 2.232208 TCGAGCATCACATGTTCAGAGT 59.768 45.455 0.00 0.00 40.07 3.24
1506 2941 3.119029 TGATCGAGCATCACATGTTCAGA 60.119 43.478 0.00 0.00 40.07 3.27
1507 2942 3.192466 TGATCGAGCATCACATGTTCAG 58.808 45.455 0.00 0.00 40.07 3.02
1508 2943 3.249986 TGATCGAGCATCACATGTTCA 57.750 42.857 0.00 0.00 40.07 3.18
1509 2944 4.510711 AGAATGATCGAGCATCACATGTTC 59.489 41.667 17.74 9.60 44.70 3.18
1511 2946 4.069300 AGAATGATCGAGCATCACATGT 57.931 40.909 17.74 0.00 44.70 3.21
1512 2947 5.007332 TGAAAGAATGATCGAGCATCACATG 59.993 40.000 17.74 0.00 44.70 3.21
1513 2948 5.007430 GTGAAAGAATGATCGAGCATCACAT 59.993 40.000 22.64 7.29 44.70 3.21
1514 2949 4.330894 GTGAAAGAATGATCGAGCATCACA 59.669 41.667 22.64 13.70 44.70 3.58
1517 2952 4.330894 TGTGTGAAAGAATGATCGAGCATC 59.669 41.667 17.74 10.45 0.00 3.91
1524 2976 5.422666 TGTGTGTGTGTGAAAGAATGATC 57.577 39.130 0.00 0.00 0.00 2.92
1577 3305 1.168714 CTCGGCTTTTCTTCCCTTGG 58.831 55.000 0.00 0.00 0.00 3.61
1591 3319 2.139118 GTTCTCATATTGGCTCTCGGC 58.861 52.381 0.00 0.00 40.90 5.54
1637 3408 2.029020 TCAAGGTCTCCGTTGTGATCTG 60.029 50.000 0.00 0.00 37.63 2.90
1646 3417 1.533469 CGGGAACTCAAGGTCTCCGT 61.533 60.000 13.56 0.00 38.05 4.69
1723 3494 4.790861 GAACCCTCCGCGTCCGAC 62.791 72.222 4.92 0.00 36.29 4.79
1745 3516 4.937620 CGTGTAGTACTACCTTGTAGACCA 59.062 45.833 26.41 4.73 35.26 4.02
1759 3530 6.793680 GCAAAAGTGGATAAAACGTGTAGTAC 59.206 38.462 0.00 0.00 0.00 2.73
1764 3535 4.911514 AGCAAAAGTGGATAAAACGTGT 57.088 36.364 0.00 0.00 0.00 4.49
1767 3538 7.646130 TGAAAGTTAGCAAAAGTGGATAAAACG 59.354 33.333 0.00 0.00 0.00 3.60
1814 5139 5.329035 AGCTGTTGAAATTGTTTGACTGT 57.671 34.783 0.00 0.00 0.00 3.55
1820 5145 7.334171 ACTGCTTTTTAGCTGTTGAAATTGTTT 59.666 29.630 0.00 0.00 42.86 2.83
1834 5407 8.803201 AGTAAGATTTTGAACTGCTTTTTAGC 57.197 30.769 0.00 0.00 0.00 3.09
1842 5415 6.729187 AGACACAAGTAAGATTTTGAACTGC 58.271 36.000 0.00 0.00 0.00 4.40
1848 5421 9.965824 ATGGTAAAAGACACAAGTAAGATTTTG 57.034 29.630 0.00 0.00 0.00 2.44
1850 5423 9.965824 CAATGGTAAAAGACACAAGTAAGATTT 57.034 29.630 0.00 0.00 0.00 2.17
1851 5424 8.576442 CCAATGGTAAAAGACACAAGTAAGATT 58.424 33.333 0.00 0.00 0.00 2.40
1854 5427 6.488683 TCCCAATGGTAAAAGACACAAGTAAG 59.511 38.462 0.00 0.00 0.00 2.34
1855 5428 6.366340 TCCCAATGGTAAAAGACACAAGTAA 58.634 36.000 0.00 0.00 0.00 2.24
1857 5430 4.798882 TCCCAATGGTAAAAGACACAAGT 58.201 39.130 0.00 0.00 0.00 3.16
1859 5432 4.586841 CCTTCCCAATGGTAAAAGACACAA 59.413 41.667 0.00 0.00 0.00 3.33
1862 5435 3.399644 TCCCTTCCCAATGGTAAAAGACA 59.600 43.478 0.00 0.00 0.00 3.41
1864 5437 4.140900 TGTTCCCTTCCCAATGGTAAAAGA 60.141 41.667 0.00 0.00 0.00 2.52
1865 5438 4.156477 TGTTCCCTTCCCAATGGTAAAAG 58.844 43.478 0.00 0.00 0.00 2.27
1905 5507 4.421479 AGCCTCTTCACCGCGACG 62.421 66.667 8.23 0.00 0.00 5.12
1911 5513 0.676151 CCTTGCTCAGCCTCTTCACC 60.676 60.000 0.00 0.00 0.00 4.02
1974 5576 2.674033 TGCTGCAGCTTGGCGATT 60.674 55.556 36.61 0.00 42.66 3.34
2048 6414 0.611714 GGTCCCTGTGTATCACCGTT 59.388 55.000 0.00 0.00 32.73 4.44
2105 6471 1.521681 GAAGTCGGCGATCTTGGGG 60.522 63.158 22.80 0.00 0.00 4.96
2296 6710 5.280945 CCACTGTCCACACATTACTTTTTG 58.719 41.667 0.00 0.00 0.00 2.44
2343 6761 3.691342 CCGACAAGACGCCCTCCA 61.691 66.667 0.00 0.00 0.00 3.86
2423 6841 4.633596 GATGCCGTCGATTGCGCG 62.634 66.667 0.00 0.00 37.46 6.86
2481 6903 4.187694 TGGTTTGGCATTGTCAGTTTTTC 58.812 39.130 0.00 0.00 0.00 2.29
2869 10843 1.671328 CTGGTGTTCTCGAGATCGCTA 59.329 52.381 27.38 23.02 39.60 4.26
2887 10864 0.392863 TCATGGTCATGGCGTTCCTG 60.393 55.000 10.61 0.00 39.24 3.86
2888 10865 0.392998 GTCATGGTCATGGCGTTCCT 60.393 55.000 10.61 0.00 39.24 3.36
2889 10866 1.376609 GGTCATGGTCATGGCGTTCC 61.377 60.000 10.61 3.72 43.98 3.62
2936 10933 0.600057 GTGCTGCTTCCCTGAAAAGG 59.400 55.000 0.00 0.00 0.00 3.11
2940 10937 1.004560 CGAGTGCTGCTTCCCTGAA 60.005 57.895 0.00 0.00 0.00 3.02
2941 10938 2.159819 GACGAGTGCTGCTTCCCTGA 62.160 60.000 0.00 0.00 0.00 3.86
2944 10941 1.605058 TAGGACGAGTGCTGCTTCCC 61.605 60.000 7.53 0.00 32.14 3.97
2990 10991 4.479158 TGCTCTACAAATCTGGGGTTTTT 58.521 39.130 0.00 0.00 0.00 1.94
3024 11027 8.475331 TCCTGTAAATACGTCTTTCATTTCTC 57.525 34.615 1.78 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.