Multiple sequence alignment - TraesCS1B01G240700

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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 TraesCS1B01G240700 chr1B 100.000 3700 0 0 1 3700 428605816 428609515 0.000000e+00 6833
1 TraesCS1B01G240700 chr1B 97.244 762 20 1 2939 3700 134731147 134730387 0.000000e+00 1290
2 TraesCS1B01G240700 chr1A 92.754 2898 115 35 1 2842 397081115 397083973 0.000000e+00 4100
3 TraesCS1B01G240700 chr1A 85.419 823 115 5 2881 3700 14105643 14104823 0.000000e+00 850
4 TraesCS1B01G240700 chr1A 78.351 194 33 7 1977 2166 236303254 236303066 2.330000e-22 117
5 TraesCS1B01G240700 chr1D 91.818 2921 110 45 1 2830 316233322 316236204 0.000000e+00 3951
6 TraesCS1B01G240700 chrUn 97.387 842 22 0 2859 3700 36775203 36774362 0.000000e+00 1434
7 TraesCS1B01G240700 chr4A 96.588 850 23 2 2856 3700 742726748 742725900 0.000000e+00 1404
8 TraesCS1B01G240700 chr4B 83.431 851 125 13 2859 3700 168966072 168965229 0.000000e+00 776
9 TraesCS1B01G240700 chr2D 83.232 823 127 10 2864 3681 498461401 498460585 0.000000e+00 745
10 TraesCS1B01G240700 chr2D 74.640 347 76 11 1829 2166 36535257 36535600 3.850000e-30 143
11 TraesCS1B01G240700 chr2D 87.234 94 8 4 1977 2068 288163029 288162938 1.820000e-18 104
12 TraesCS1B01G240700 chr7A 86.289 671 86 5 3033 3700 696856872 696856205 0.000000e+00 725
13 TraesCS1B01G240700 chr4D 84.175 733 105 10 2973 3700 420931962 420931236 0.000000e+00 701
14 TraesCS1B01G240700 chr4D 87.629 97 8 4 1974 2068 188963040 188963134 3.910000e-20 110
15 TraesCS1B01G240700 chr5D 84.218 697 101 8 3008 3700 396985954 396985263 0.000000e+00 669
16 TraesCS1B01G240700 chr5D 83.929 168 21 6 1552 1716 521261160 521260996 4.950000e-34 156
17 TraesCS1B01G240700 chr3A 84.387 269 39 2 2863 3131 117242192 117241927 1.020000e-65 261
18 TraesCS1B01G240700 chr2A 75.645 349 69 15 1829 2166 40537659 40538002 3.820000e-35 159
19 TraesCS1B01G240700 chr5A 83.234 167 24 4 1552 1716 649643113 649642949 2.300000e-32 150
20 TraesCS1B01G240700 chr5B 82.530 166 25 4 1553 1716 657419753 657419590 3.850000e-30 143
21 TraesCS1B01G240700 chr5B 77.436 195 34 8 1977 2166 634280023 634279834 1.410000e-19 108
22 TraesCS1B01G240700 chr2B 74.785 349 72 13 1829 2166 62546776 62547119 3.850000e-30 143


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 TraesCS1B01G240700 chr1B 428605816 428609515 3699 False 6833 6833 100.000 1 3700 1 chr1B.!!$F1 3699
1 TraesCS1B01G240700 chr1B 134730387 134731147 760 True 1290 1290 97.244 2939 3700 1 chr1B.!!$R1 761
2 TraesCS1B01G240700 chr1A 397081115 397083973 2858 False 4100 4100 92.754 1 2842 1 chr1A.!!$F1 2841
3 TraesCS1B01G240700 chr1A 14104823 14105643 820 True 850 850 85.419 2881 3700 1 chr1A.!!$R1 819
4 TraesCS1B01G240700 chr1D 316233322 316236204 2882 False 3951 3951 91.818 1 2830 1 chr1D.!!$F1 2829
5 TraesCS1B01G240700 chrUn 36774362 36775203 841 True 1434 1434 97.387 2859 3700 1 chrUn.!!$R1 841
6 TraesCS1B01G240700 chr4A 742725900 742726748 848 True 1404 1404 96.588 2856 3700 1 chr4A.!!$R1 844
7 TraesCS1B01G240700 chr4B 168965229 168966072 843 True 776 776 83.431 2859 3700 1 chr4B.!!$R1 841
8 TraesCS1B01G240700 chr2D 498460585 498461401 816 True 745 745 83.232 2864 3681 1 chr2D.!!$R2 817
9 TraesCS1B01G240700 chr7A 696856205 696856872 667 True 725 725 86.289 3033 3700 1 chr7A.!!$R1 667
10 TraesCS1B01G240700 chr4D 420931236 420931962 726 True 701 701 84.175 2973 3700 1 chr4D.!!$R1 727
11 TraesCS1B01G240700 chr5D 396985263 396985954 691 True 669 669 84.218 3008 3700 1 chr5D.!!$R1 692

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
175 202 0.110056 GATGGAATTATGCAGCCGCG 60.110 55.0 0.0 0.0 42.97 6.46 F
277 304 0.393808 ACCAACCACGCTTGTTCTGT 60.394 50.0 0.0 0.0 0.00 3.41 F
1150 1232 0.179048 TATGATGGTGAAGGCGCCTG 60.179 55.0 33.6 0.0 45.15 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1131 1213 0.179048 CAGGCGCCTTCACCATCATA 60.179 55.0 30.60 0.0 0.0 2.15 R
1802 1895 0.320858 TCGGGTTGAAACTGCGCATA 60.321 50.0 12.24 0.0 0.0 3.14 R
2845 2953 0.037697 GCCCATCGCCGTATACATCA 60.038 55.0 3.32 0.0 0.0 3.07 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
58 62 6.901081 ACATAAAAAGGTGAAGAGGAAAGG 57.099 37.500 0.00 0.00 0.00 3.11
169 186 7.415592 TGGTTAATTGTGATGGAATTATGCA 57.584 32.000 0.00 0.00 0.00 3.96
175 202 0.110056 GATGGAATTATGCAGCCGCG 60.110 55.000 0.00 0.00 42.97 6.46
240 267 8.389354 ACAGTTGGTTTATCAGCATTACTGTGT 61.389 37.037 9.57 0.00 46.30 3.72
247 274 3.389741 GCATTACTGTGTGCTGTGC 57.610 52.632 11.27 0.00 38.30 4.57
248 275 0.877071 GCATTACTGTGTGCTGTGCT 59.123 50.000 11.27 0.00 38.30 4.40
249 276 1.400629 GCATTACTGTGTGCTGTGCTG 60.401 52.381 11.27 0.00 38.30 4.41
250 277 1.875514 CATTACTGTGTGCTGTGCTGT 59.124 47.619 0.00 0.00 0.00 4.40
251 278 1.298602 TTACTGTGTGCTGTGCTGTG 58.701 50.000 0.00 0.00 0.00 3.66
277 304 0.393808 ACCAACCACGCTTGTTCTGT 60.394 50.000 0.00 0.00 0.00 3.41
284 311 3.131396 CCACGCTTGTTCTGTAAGTCTT 58.869 45.455 0.00 0.00 33.76 3.01
380 411 2.565841 ACTCAGAGTTGCACTTGTTCC 58.434 47.619 0.00 0.00 0.00 3.62
423 454 3.685139 TCAAGCCGTCAGATTCTTCTT 57.315 42.857 0.00 0.00 0.00 2.52
531 562 8.786898 ACTATGCGTTATGATGAAGCATAATTT 58.213 29.630 15.89 4.38 46.07 1.82
585 616 6.293516 CGACAGACTACCTGATAGTTGGTATC 60.294 46.154 0.00 0.00 44.64 2.24
594 625 2.973694 TAGTTGGTATCGGTTCCTGC 57.026 50.000 0.00 0.00 0.00 4.85
600 631 3.239449 TGGTATCGGTTCCTGCAGATAT 58.761 45.455 17.39 1.71 30.67 1.63
623 654 2.097825 GGTAGAGCGAGGAAGGTACAA 58.902 52.381 0.00 0.00 0.00 2.41
624 655 2.694109 GGTAGAGCGAGGAAGGTACAAT 59.306 50.000 0.00 0.00 0.00 2.71
625 656 2.969628 AGAGCGAGGAAGGTACAATG 57.030 50.000 0.00 0.00 0.00 2.82
627 658 0.905357 AGCGAGGAAGGTACAATGCT 59.095 50.000 0.00 0.00 0.00 3.79
657 696 6.810676 AGTACATAAATAGATGCAGATCAGCG 59.189 38.462 5.56 0.00 35.94 5.18
685 727 1.523154 GCCGATGAAACAGGCCAACA 61.523 55.000 5.01 0.00 44.80 3.33
784 829 1.208052 GCCAATAGCCACTGAGTGAGA 59.792 52.381 15.33 0.00 35.23 3.27
785 830 2.355108 GCCAATAGCCACTGAGTGAGAA 60.355 50.000 15.33 0.00 35.23 2.87
786 831 3.529533 CCAATAGCCACTGAGTGAGAAG 58.470 50.000 15.33 0.00 35.23 2.85
788 833 4.180057 CAATAGCCACTGAGTGAGAAGAC 58.820 47.826 15.33 0.00 35.23 3.01
790 835 2.042464 AGCCACTGAGTGAGAAGACAA 58.958 47.619 15.33 0.00 35.23 3.18
791 836 2.139118 GCCACTGAGTGAGAAGACAAC 58.861 52.381 15.33 0.00 35.23 3.32
792 837 2.760374 CCACTGAGTGAGAAGACAACC 58.240 52.381 15.33 0.00 35.23 3.77
793 838 2.548920 CCACTGAGTGAGAAGACAACCC 60.549 54.545 15.33 0.00 35.23 4.11
794 839 2.103094 CACTGAGTGAGAAGACAACCCA 59.897 50.000 6.79 0.00 35.23 4.51
795 840 2.366916 ACTGAGTGAGAAGACAACCCAG 59.633 50.000 0.00 0.00 0.00 4.45
796 841 2.366916 CTGAGTGAGAAGACAACCCAGT 59.633 50.000 0.00 0.00 0.00 4.00
797 842 2.771943 TGAGTGAGAAGACAACCCAGTT 59.228 45.455 0.00 0.00 0.00 3.16
798 843 3.181465 TGAGTGAGAAGACAACCCAGTTC 60.181 47.826 0.00 0.00 0.00 3.01
799 844 2.771943 AGTGAGAAGACAACCCAGTTCA 59.228 45.455 0.00 0.00 0.00 3.18
800 845 3.134458 GTGAGAAGACAACCCAGTTCAG 58.866 50.000 0.00 0.00 0.00 3.02
801 846 3.038280 TGAGAAGACAACCCAGTTCAGA 58.962 45.455 0.00 0.00 0.00 3.27
802 847 3.181465 TGAGAAGACAACCCAGTTCAGAC 60.181 47.826 0.00 0.00 0.00 3.51
803 848 2.771943 AGAAGACAACCCAGTTCAGACA 59.228 45.455 0.00 0.00 0.00 3.41
804 849 3.392616 AGAAGACAACCCAGTTCAGACAT 59.607 43.478 0.00 0.00 0.00 3.06
805 850 3.864789 AGACAACCCAGTTCAGACATT 57.135 42.857 0.00 0.00 0.00 2.71
806 851 3.744660 AGACAACCCAGTTCAGACATTC 58.255 45.455 0.00 0.00 0.00 2.67
835 880 5.920193 TCTCTTGCTTTTGGGATTAATGG 57.080 39.130 0.00 0.00 0.00 3.16
840 885 4.163427 TGCTTTTGGGATTAATGGGTTCA 58.837 39.130 0.00 0.00 0.00 3.18
1062 1126 1.735360 GAACTTTGCACTGCTGCCA 59.265 52.632 1.98 0.00 43.51 4.92
1131 1213 3.708631 GGATCATCATATCGACCAGGGAT 59.291 47.826 0.00 0.00 0.00 3.85
1132 1214 4.895889 GGATCATCATATCGACCAGGGATA 59.104 45.833 0.00 0.00 0.00 2.59
1133 1215 5.541868 GGATCATCATATCGACCAGGGATAT 59.458 44.000 0.00 0.00 37.53 1.63
1150 1232 0.179048 TATGATGGTGAAGGCGCCTG 60.179 55.000 33.60 0.00 45.15 4.85
1151 1233 3.512516 GATGGTGAAGGCGCCTGC 61.513 66.667 33.60 31.17 45.15 4.85
1327 1412 2.809601 GTCGACATTCGGCGCACT 60.810 61.111 11.55 0.00 40.88 4.40
1738 1830 0.248949 GTACGCCGTCTCCCATCTTC 60.249 60.000 0.00 0.00 0.00 2.87
1757 1849 6.672266 TCTTCTCTATTCTTCCGCCATTAT 57.328 37.500 0.00 0.00 0.00 1.28
1759 1851 5.060662 TCTCTATTCTTCCGCCATTATCG 57.939 43.478 0.00 0.00 0.00 2.92
1760 1852 4.523173 TCTCTATTCTTCCGCCATTATCGT 59.477 41.667 0.00 0.00 0.00 3.73
1761 1853 4.556233 TCTATTCTTCCGCCATTATCGTG 58.444 43.478 0.00 0.00 0.00 4.35
1762 1854 2.971660 TTCTTCCGCCATTATCGTGA 57.028 45.000 0.00 0.00 0.00 4.35
1763 1855 2.218953 TCTTCCGCCATTATCGTGAC 57.781 50.000 0.00 0.00 0.00 3.67
1764 1856 0.852777 CTTCCGCCATTATCGTGACG 59.147 55.000 0.00 0.00 0.00 4.35
1778 1870 1.979155 TGACGGGACTCCTCTGCTG 60.979 63.158 0.00 0.00 0.00 4.41
1802 1895 0.982704 AACCTCTCTCTGCTGCATGT 59.017 50.000 1.31 0.00 0.00 3.21
1931 2024 4.530857 CAGTCCGCCATCCCGTCC 62.531 72.222 0.00 0.00 0.00 4.79
2103 2196 4.393155 TGCGCAACGGCTCCATCT 62.393 61.111 8.16 0.00 38.10 2.90
2116 2209 3.716195 CATCTCCCACCACGGCCA 61.716 66.667 2.24 0.00 0.00 5.36
2190 2283 4.704833 GGCTGCGCTTCAGGGTCA 62.705 66.667 9.73 0.00 43.06 4.02
2297 2390 1.302832 GCAGTGGGTGAGGGACAAG 60.303 63.158 0.00 0.00 0.00 3.16
2708 2801 6.156949 AGCTCTTCTACCCTTGATCACATTTA 59.843 38.462 0.00 0.00 0.00 1.40
2709 2802 6.481644 GCTCTTCTACCCTTGATCACATTTAG 59.518 42.308 0.00 0.00 0.00 1.85
2739 2843 6.113411 ACTTACTAGGTTGTGATAACCATGC 58.887 40.000 13.68 0.00 42.69 4.06
2744 2848 3.511146 AGGTTGTGATAACCATGCCAAAG 59.489 43.478 13.68 0.00 42.69 2.77
2745 2849 3.258123 GGTTGTGATAACCATGCCAAAGT 59.742 43.478 6.21 0.00 40.03 2.66
2746 2850 4.461081 GGTTGTGATAACCATGCCAAAGTA 59.539 41.667 6.21 0.00 40.03 2.24
2749 2857 5.321102 TGTGATAACCATGCCAAAGTAGTT 58.679 37.500 0.00 0.00 0.00 2.24
2764 2872 0.627451 TAGTTGAGTAGGCCTCCCGA 59.373 55.000 9.68 0.00 39.65 5.14
2765 2873 0.684805 AGTTGAGTAGGCCTCCCGAG 60.685 60.000 9.68 0.00 39.65 4.63
2766 2874 0.971447 GTTGAGTAGGCCTCCCGAGT 60.971 60.000 9.68 0.00 39.65 4.18
2842 2950 2.757314 GCCTTAAGAAGAAGCTGCCAAT 59.243 45.455 3.36 0.00 0.00 3.16
2843 2951 3.428589 GCCTTAAGAAGAAGCTGCCAATG 60.429 47.826 3.36 0.00 0.00 2.82
2844 2952 4.012374 CCTTAAGAAGAAGCTGCCAATGA 58.988 43.478 3.36 0.00 0.00 2.57
2845 2953 4.643784 CCTTAAGAAGAAGCTGCCAATGAT 59.356 41.667 3.36 0.00 0.00 2.45
2846 2954 5.450137 CCTTAAGAAGAAGCTGCCAATGATG 60.450 44.000 3.36 0.00 0.00 3.07
2847 2955 3.361281 AGAAGAAGCTGCCAATGATGA 57.639 42.857 0.00 0.00 0.00 2.92
2848 2956 3.899726 AGAAGAAGCTGCCAATGATGAT 58.100 40.909 0.00 0.00 0.00 2.45
2849 2957 3.632604 AGAAGAAGCTGCCAATGATGATG 59.367 43.478 0.00 0.00 0.00 3.07
2850 2958 3.014304 AGAAGCTGCCAATGATGATGT 57.986 42.857 0.00 0.00 0.00 3.06
2851 2959 4.160642 AGAAGCTGCCAATGATGATGTA 57.839 40.909 0.00 0.00 0.00 2.29
2852 2960 4.726583 AGAAGCTGCCAATGATGATGTAT 58.273 39.130 0.00 0.00 0.00 2.29
2853 2961 5.872963 AGAAGCTGCCAATGATGATGTATA 58.127 37.500 0.00 0.00 0.00 1.47
2854 2962 5.704515 AGAAGCTGCCAATGATGATGTATAC 59.295 40.000 0.00 0.00 0.00 1.47
3402 3521 2.504244 GCGTTCGTCGACCTCCAG 60.504 66.667 10.58 0.00 42.86 3.86
3446 3565 4.849310 GCTCCGCCCACCGCATTA 62.849 66.667 0.00 0.00 37.30 1.90
3487 3606 4.396271 TTTCCGGCCAATCGCGGA 62.396 61.111 6.13 0.00 40.13 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 62 2.617308 CAACAGGCATCATGTCCATCTC 59.383 50.000 0.00 0.00 0.00 2.75
175 202 1.678425 CCAAGAGAGCTGGAAAGAGCC 60.678 57.143 0.00 0.00 40.08 4.70
240 267 1.451072 TGATCCACACAGCACAGCA 59.549 52.632 0.00 0.00 0.00 4.41
241 268 4.384599 TGATCCACACAGCACAGC 57.615 55.556 0.00 0.00 0.00 4.40
264 291 3.555956 ACAAGACTTACAGAACAAGCGTG 59.444 43.478 0.00 0.00 0.00 5.34
277 304 6.425721 CCGAAACTAATCCACAACAAGACTTA 59.574 38.462 0.00 0.00 0.00 2.24
284 311 2.811431 CAGCCGAAACTAATCCACAACA 59.189 45.455 0.00 0.00 0.00 3.33
317 344 2.309613 TGCATTTTTCTCTGCACCAGT 58.690 42.857 0.00 0.00 43.11 4.00
328 356 8.301730 TGAGAACAAGATGAAATGCATTTTTC 57.698 30.769 24.81 22.10 37.34 2.29
380 411 0.734889 CATCCTAAACAGGGCTTGCG 59.265 55.000 0.00 0.00 0.00 4.85
388 419 3.313526 CGGCTTGAATCCATCCTAAACAG 59.686 47.826 0.00 0.00 0.00 3.16
423 454 8.602424 TGATTTTCTTCTTACATTCCACCTCTA 58.398 33.333 0.00 0.00 0.00 2.43
531 562 4.002316 GGCAAAATGGAAAATAAGCAGCA 58.998 39.130 0.00 0.00 0.00 4.41
585 616 1.971357 ACCCTATATCTGCAGGAACCG 59.029 52.381 15.13 0.03 33.42 4.44
594 625 4.223556 TCCTCGCTCTACCCTATATCTG 57.776 50.000 0.00 0.00 0.00 2.90
600 631 0.924823 ACCTTCCTCGCTCTACCCTA 59.075 55.000 0.00 0.00 0.00 3.53
623 654 8.150296 TGCATCTATTTATGTACTGTACAGCAT 58.850 33.333 22.90 19.37 42.77 3.79
624 655 7.496747 TGCATCTATTTATGTACTGTACAGCA 58.503 34.615 22.90 19.62 42.77 4.41
625 656 7.867909 TCTGCATCTATTTATGTACTGTACAGC 59.132 37.037 22.90 17.67 42.77 4.40
627 658 9.914131 GATCTGCATCTATTTATGTACTGTACA 57.086 33.333 21.68 21.68 43.80 2.90
645 684 2.053259 ATCCTGCCGCTGATCTGCAT 62.053 55.000 22.44 6.25 34.41 3.96
685 727 3.648339 AAGTGCATCAAAATCAAGCGT 57.352 38.095 0.00 0.00 0.00 5.07
784 829 3.864789 ATGTCTGAACTGGGTTGTCTT 57.135 42.857 0.00 0.00 0.00 3.01
785 830 3.392616 AGAATGTCTGAACTGGGTTGTCT 59.607 43.478 0.00 0.00 0.00 3.41
786 831 3.744660 AGAATGTCTGAACTGGGTTGTC 58.255 45.455 0.00 0.00 0.00 3.18
788 833 3.743521 TGAGAATGTCTGAACTGGGTTG 58.256 45.455 0.00 0.00 0.00 3.77
790 835 2.975489 ACTGAGAATGTCTGAACTGGGT 59.025 45.455 0.00 0.00 0.00 4.51
791 836 3.692257 ACTGAGAATGTCTGAACTGGG 57.308 47.619 0.00 0.00 0.00 4.45
792 837 5.303971 AGAAACTGAGAATGTCTGAACTGG 58.696 41.667 0.00 0.00 0.00 4.00
793 838 6.222389 AGAGAAACTGAGAATGTCTGAACTG 58.778 40.000 0.00 0.00 0.00 3.16
794 839 6.418057 AGAGAAACTGAGAATGTCTGAACT 57.582 37.500 0.00 0.00 0.00 3.01
795 840 6.565623 GCAAGAGAAACTGAGAATGTCTGAAC 60.566 42.308 0.00 0.00 0.00 3.18
796 841 5.468072 GCAAGAGAAACTGAGAATGTCTGAA 59.532 40.000 0.00 0.00 0.00 3.02
797 842 4.993584 GCAAGAGAAACTGAGAATGTCTGA 59.006 41.667 0.00 0.00 0.00 3.27
798 843 4.996122 AGCAAGAGAAACTGAGAATGTCTG 59.004 41.667 0.00 0.00 0.00 3.51
799 844 5.226194 AGCAAGAGAAACTGAGAATGTCT 57.774 39.130 0.00 0.00 0.00 3.41
800 845 5.938438 AAGCAAGAGAAACTGAGAATGTC 57.062 39.130 0.00 0.00 0.00 3.06
801 846 6.460676 CCAAAAGCAAGAGAAACTGAGAATGT 60.461 38.462 0.00 0.00 0.00 2.71
802 847 5.919141 CCAAAAGCAAGAGAAACTGAGAATG 59.081 40.000 0.00 0.00 0.00 2.67
803 848 5.010415 CCCAAAAGCAAGAGAAACTGAGAAT 59.990 40.000 0.00 0.00 0.00 2.40
804 849 4.339247 CCCAAAAGCAAGAGAAACTGAGAA 59.661 41.667 0.00 0.00 0.00 2.87
805 850 3.885297 CCCAAAAGCAAGAGAAACTGAGA 59.115 43.478 0.00 0.00 0.00 3.27
806 851 3.885297 TCCCAAAAGCAAGAGAAACTGAG 59.115 43.478 0.00 0.00 0.00 3.35
835 880 1.723870 GCGGATCACATGCTGAACC 59.276 57.895 11.85 11.85 38.27 3.62
840 885 3.974835 TTGGCGCGGATCACATGCT 62.975 57.895 8.83 0.00 0.00 3.79
1062 1126 1.439228 CGGAGAGCGTGATGATGGT 59.561 57.895 0.00 0.00 0.00 3.55
1131 1213 0.179048 CAGGCGCCTTCACCATCATA 60.179 55.000 30.60 0.00 0.00 2.15
1132 1214 1.452651 CAGGCGCCTTCACCATCAT 60.453 57.895 30.60 0.00 0.00 2.45
1133 1215 2.046023 CAGGCGCCTTCACCATCA 60.046 61.111 30.60 0.00 0.00 3.07
1150 1232 3.827898 CGAGGACGAGGAGTGGGC 61.828 72.222 0.00 0.00 42.66 5.36
1151 1233 3.141488 CCGAGGACGAGGAGTGGG 61.141 72.222 0.00 0.00 42.66 4.61
1301 1383 1.153745 GAATGTCGACCAGCTCGCT 60.154 57.895 14.12 0.00 42.62 4.93
1738 1830 4.623167 CACGATAATGGCGGAAGAATAGAG 59.377 45.833 0.00 0.00 0.00 2.43
1757 1849 1.674651 CAGAGGAGTCCCGTCACGA 60.675 63.158 5.25 0.00 37.58 4.35
1759 1851 1.979693 AGCAGAGGAGTCCCGTCAC 60.980 63.158 5.25 0.00 37.58 3.67
1760 1852 1.979155 CAGCAGAGGAGTCCCGTCA 60.979 63.158 5.25 0.00 37.58 4.35
1761 1853 1.251527 TTCAGCAGAGGAGTCCCGTC 61.252 60.000 5.25 0.00 37.58 4.79
1762 1854 1.228894 TTCAGCAGAGGAGTCCCGT 60.229 57.895 5.25 0.00 37.58 5.28
1763 1855 1.216710 GTTCAGCAGAGGAGTCCCG 59.783 63.158 5.25 0.00 37.58 5.14
1764 1856 1.853963 TAGTTCAGCAGAGGAGTCCC 58.146 55.000 5.25 0.00 0.00 4.46
1778 1870 2.232452 TGCAGCAGAGAGAGGTTAGTTC 59.768 50.000 0.00 0.00 0.00 3.01
1802 1895 0.320858 TCGGGTTGAAACTGCGCATA 60.321 50.000 12.24 0.00 0.00 3.14
1811 1904 1.573829 GCATCTGCGTCGGGTTGAAA 61.574 55.000 0.00 0.00 0.00 2.69
1931 2024 3.330720 AAGGACTTGGCCTCCGGG 61.331 66.667 3.32 0.00 37.26 5.73
2230 2323 3.299977 CCTCGGTCGACACCCACA 61.300 66.667 18.91 0.00 40.01 4.17
2297 2390 2.154462 CTGGTGGTGTTGAAGTCCATC 58.846 52.381 0.00 0.00 33.68 3.51
2708 2801 9.702494 GTTATCACAACCTAGTAAGTAAACACT 57.298 33.333 0.00 0.00 0.00 3.55
2709 2802 8.929746 GGTTATCACAACCTAGTAAGTAAACAC 58.070 37.037 0.00 0.00 37.34 3.32
2739 2843 3.863041 GAGGCCTACTCAACTACTTTGG 58.137 50.000 4.42 0.00 45.85 3.28
2842 2950 2.094234 CCCATCGCCGTATACATCATCA 60.094 50.000 3.32 0.00 0.00 3.07
2843 2951 2.540515 CCCATCGCCGTATACATCATC 58.459 52.381 3.32 0.00 0.00 2.92
2844 2952 1.405526 GCCCATCGCCGTATACATCAT 60.406 52.381 3.32 0.00 0.00 2.45
2845 2953 0.037697 GCCCATCGCCGTATACATCA 60.038 55.000 3.32 0.00 0.00 3.07
2846 2954 1.076533 CGCCCATCGCCGTATACATC 61.077 60.000 3.32 0.00 0.00 3.06
2847 2955 1.080093 CGCCCATCGCCGTATACAT 60.080 57.895 3.32 0.00 0.00 2.29
2848 2956 2.194889 TCGCCCATCGCCGTATACA 61.195 57.895 3.32 0.00 38.27 2.29
2849 2957 1.731969 GTCGCCCATCGCCGTATAC 60.732 63.158 0.00 0.00 38.27 1.47
2850 2958 1.900016 AGTCGCCCATCGCCGTATA 60.900 57.895 0.00 0.00 38.27 1.47
2851 2959 3.224324 AGTCGCCCATCGCCGTAT 61.224 61.111 0.00 0.00 38.27 3.06
2852 2960 4.201679 CAGTCGCCCATCGCCGTA 62.202 66.667 0.00 0.00 38.27 4.02
3487 3606 1.997874 GGAGGGGAGAGTGGCACAT 60.998 63.158 21.41 7.84 44.52 3.21


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

AutoCloner maintained by Alex Coulton.